Compositions and Methods for Degradation of Misfolded Proteins

ABSTRACT

The present invention relates to compositions and methods for promoting the degradation of misfolded proteins and protein aggregates. The compositions and methods may be used to treat a disorder associated with misfolded proteins or protein aggregates. In certain instances, the compositions and methods relate to modulators of one or more TRIM proteins or one or more STUbLs.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/577,915, filed Nov. 29, 2017, which is the U.S. national phaseapplication filed under 35 U.S.C. § 371 claiming benefit toInternational Patent application No. PCT/US2016/034751, filed on May 27,2016, which is entitled to priority under 35 U.S.C. § 119(e) to U.S.Provisional Patent Application No. 62/168,309 filed on May 29, 2015, thecontents of which are incorporated by reference herein in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under CA088868,GM060911, CA182675, CA184867, and P30 AI045008, awarded by the NationalInstitute of Health. The government has certain rights in the invention.

REFERENCE TO A “SEQUENCE LISTING”, A TABLE OR A COMPUTER PROGRAM LISTINGAPPENDIX SUBMITTED AS AN XML FILE

The present application hereby incorporates by reference the entirecontents of the XML file named “046483-6149-01US_SequenceListing.xml” inXML format, which was created on Nov. 21, 2022, and is 327,360 bytes insize.

BACKGROUND OF THE INVENTION

Proteins are the most abundant macromolecules of the cell and arecritical to virtually all physiological processes. To perform theirbiological functions, the majority of proteins need to fold into andmaintain their native conformations. Although the native conformation ofa protein is determined by its amino acid sequence, the folding processis extraordinarily complex and highly prone to error, and its utilitycan be further limited in situations of genetic mutations, biogeneticinaccuracies, and posttranslational damages (Dobson, 2003, Nature, 426:884-890; Goldberg, 2003, Nature, 426: 895-899). Proteins that haveadopted aberrant conformations, and the aggregates formed by them, posea constant threat to cell viability and function. Failure to eliminatethese proteins is closely linked to the pathogenesis of variousdebilitating human diseases (Selkoe, 2003, Nature, 426: 900-904; Tayloret al., 2002, Science, 296: 1991-1995)

To contend with protein misfolding, cells employ two broad sets ofprotein quality control (PQC) systems: systems that assist proteins inachieving their native conformations, and systems that eliminatemisfolded proteins once they are formed. The former consist mainly of alarge number of molecular chaperones and their cochaperones, which in anATP-dependent manner protect proteins in their nonnative state andreduce misfolding and aggregation. Notable examples include (1) heatshock protein 70 (Hsp70), which aids the folding of a wide range ofproteins; (2) Hsp60/chaperonin, which forms a macromolecular cage toencapsulate relatively small proteins for uninterrupted folding; and (3)HSP90, which most commonly acts on proteins involved in cell signalingand transcription (Hartl et al., 2011, Nature, 475: 324-332).

Systems that remove misfolded proteins include protein disaggregases.For example, Hsp100 proteins in prokaryotes or lower eukaryotes (e.g.,ClpB in bacteria and Hsp104 in yeast) can resolubilize proteinaggregates, functioning in concert with Hsp70 and its cochaperone Hsp40(Glover and Linquist, 1998, Cell, 94: 73-82). Nevertheless, given thatprotein misfolding is inevitable and often cannot be reversed due tomutations, biogenetic errors, or irreparable damages, cells ultimatelyrely on degradative systems to maintain protein quality. Yet, thesesystems are still poorly understood. Although the ubiquitin-proteasomepathway, along with autophagy, must be an important part of thesesystems, the critical issue of how they selectively recognize misfoldedproteins and target them for degradation remains elusive (Goldberg,2003, Nature, 426: 895-899; Tyedmers et al, 2010, Nat Rev Mol Cell Biol,11: 777-788).

Furthermore, compared to the other cellular compartments such as theendoplasmic reticulum (Buchberger et al., 2010, Mol Cell, 40: 238-252),the PQC systems in the nucleus are conspicuously unclear. Misfoldedproteins in the nucleus can be particularly damaging to postmitoticmammalian cells (e.g., neurons and cardiac myocytes), which are unableto remove these proteins through the breakdown of the nuclear envelopeduring mitosis. The importance of understanding PQC in this cellularcompartment is emphasized by the formation of neuronal intranuclearinclusions that are associated with various dominantly inheritedneurodegenerative diseases, including Huntington's disease (HD) andseveral types of spinocerebellar ataxias (SCAs). These diseases arecaused by an expansion within the relevant genes of a CAG repeat, whichencodes a polyQ stretch. They are manifested when the polyQ stretchexceeds a threshold length that is disease specific, and becomeprogressively more severe as its length increases (Orr and Zoghbi, 2007,Annu Rev Neurosci, 30: 575-621).

Thus, there is a need in the art for compositions and methods foreliminating misfolded proteins. The present invention satisfies thisunmet need.

SUMMARY OF THE INVENTION

In one aspect, the present invention provides a composition for treatingor preventing a disease or disorder associated with misfolded protein orprotein aggregates, wherein the composition comprises a modulator of oneor more TRIM proteins. In one embodiment, the modulator increases theexpression or activity of the one or more TRIM proteins. In oneembodiment, the modulator is at least one of a chemical compound, aprotein, a peptide, a peptidomemetic, an antibody, a ribozyme, a smallmolecule chemical compound, a nucleic acid, a vector, and an antisensenucleic acid.

In one embodiment, the modulator increases the expression or activity ofat least one of human TRIM3, TRIM4, TRIM5, TRIM6, TRIM7, TRIM9, TRIM11,TRIM13, TRIM14, TRIM15, TRIM16, TRIM17, TRIM19 (also referred to hereinas “PML”), TRIM20, TRIM21, TRIM24, TRIM25, TRIM27, TRIM28, TRIM29,TRIM32, TRIM34, TRIM39, TRIM43, TRIM44, TRIM45, TRIM46, TRIM49, TRIM50,TRIM52, TRIM58, TRIM59, TRIM65, TRIM67, TRIM69, TRIM70, TRIM74 andTRIM75; and mouse TRIM30.

In one embodiment, the composition comprises an isolated peptidecomprising one or more TRIM proteins. In one embodiment, the isolatedpeptide further comprises a cell penetrating peptide (CPP) to allow forentry of the isolated peptide into a cell. In one embodiment, the CPPcomprises the protein transduction domain of HIV tat.

In one embodiment, the composition comprises an isolated nucleic acidmolecule encoding one or more TRIM proteins.

In one embodiment, the disease or disorder is a polyQ disorder. In oneembodiment, the disease or disorder is a neurodegenerative disease ordisorder selected from the group consisting of Spinocerebellar ataxia(SCA) Type 1 (SCA1), SCA2, SCA3, SCA6, SCA7, SCA17, Huntington'sdisease, Dentatorubral-pallidoluysian atrophy (DRPLA), Alzheimer'sdisease, Parkinson's disease, amyotrophic lateral sclerosis (ALS), atransmissible spongiform encephalopathy (prion disease), a tauopathy,and Frontotemporal lobar degeneration (FTLD). In one embodiment, thedisease or disorder is selected from the group consisting of ALamyloidosis, AA amyloidosis, Familial Mediterranean fever, senilesystemic amyloidosis, familial amyloidotic polyneuropathy,hemodialysis-related amyloidosis, ApoAI amyloidosis, ApoAII amyloidosis,ApoAIV amyloidosis, Finnish hereditary amyloidosis, lysozymeamyloidosis, fibrinogen amyloidosis, Icelandic hereditary cerebralamyloid angiopathy, type II diabetes, medullary carcinoma of thethyroid, atrial amyloidosis, hereditary cerebral hemorrhage withamyloidosis, pituitary prolactinoma, injection-localized amyloidosis,aortic medial amyloidosis, hereditary lattice corneal dystrophy, cornealamyloidosis associated with trichiasis, cataract, calcifying epithelialodontogenic tumor, pulmonary alveolar proteinosis, inclusion-bodymyostis, and cuteaneous lichen amyloidosis. In one embodiment, thedisease or disorder is cancer associated with p53 mutant aggregates.

In one aspect, the present invention provides a method for treating orpreventing a disease or disorder associated with misfolded protein orprotein aggregates in a subject in need thereof, where the methodcomprises administering to the subject a composition comprising amodulator of one or more TRIM proteins. In one embodiment, the modulatorincreases the expression or activity of the one or more TRIM proteins.In one embodiment, the modulator is at least one of a chemical compound,a protein, a peptide, a peptidomemetic, an antibody, a ribozyme, a smallmolecule chemical compound, a nucleic acid, a vector, and an antisensenucleic acid.

In one embodiment, the modulator increases the expression or activity ofat least one of human TRIM3, TRIM4, TRIM5, TRIM6, TRIM7, TRIM9, TRIM11,TRIM13, TRIM14, TRIM15, TRIM16, TRIM17, TRIM19 (also referred to hereinas “PML”), TRIM20, TRIM21, TRIM24, TRIM25, TRIM27, TRIM28, TRIM29,TRIM32, TRIM34, TRIM39, TRIM43, TRIM44, TRIM45, TRIM46, TRIM49, TRIM50,TRIM52, TRIM58, TRIM59, TRIM65, TRIM67, TRIM69, TRIM70, TRIM74 andTRIM75; and mouse TRIM30.

In one embodiment, the composition comprises an isolated peptidecomprising one or more TRIM proteins. In one embodiment, the isolatedpeptide further comprises a cell penetrating peptide (CPP) to allow forentry of the isolated peptide into a cell. In one embodiment, the CPPcomprises the protein transduction domain of HIV tat.

In one embodiment, the composition comprises an isolated nucleic acidmolecule encoding one or more TRIM proteins.

In one embodiment, the disease or disorder is a polyQ disorder. In oneembodiment, the disease or disorder is a neurodegenerative disease ordisorder selected from the group consisting of Spinocerebellar ataxia(SCA) Type 1 (SCA1), SCA2, SCA3, SCA6, SCA7, SCA17, Huntington'sdisease, Dentatorubral-pallidoluysian atrophy (DRPLA), Alzheimer'sdisease, Parkinson's disease, amyotrophic lateral sclerosis (ALS), atransmissible spongiform encephalopathy (prion disease), a tauopathy,and Frontotemporal lobar degeneration (FTLD). In one embodiment, thedisease or disorder is selected from the group consisting of ALamyloidosis, AA amyloidosis, Familial Mediterranean fever, senilesystemic amyloidosis, familial amyloidotic polyneuropathy,hemodialysis-related amyloidosis, ApoAI amyloidosis, ApoAII amyloidosis,ApoAIV amyloidosis, Finnish hereditary amyloidosis, lysozymeamyloidosis, fibrinogen amyloidosis, Icelandic hereditary cerebralamyloid angiopathy, type II diabetes, medullary carcinoma of thethyroid, atrial amyloidosis, hereditary cerebral hemorrhage withamyloidosis, pituitary prolactinoma, injection-localized amyloidosis,aortic medial amyloidosis, hereditary lattice corneal dystrophy, cornealamyloidosis associated with trichiasis, cataract, calcifying epithelialodontogenic tumor, pulmonary alveolar proteinosis, inclusion-bodymyostis, and cuteaneous lichen amyloidosis. In one embodiment, thedisease or disorder is cancer associated with p53 mutant aggregates.

In one embodiment, the method comprises administering the composition toat least one neural cell of the subject.

In one aspect, the present invention provides a composition for treatingor preventing a disease or disorder associated with degradation offunctional mutant protein, where the composition comprises a modulatorof one or more TRIM proteins. In one embodiment, the modulator increasesthe expression or activity of the one or more TRIM proteins. In oneembodiment, the modulator is at least one of the group consisting of achemical compound, a protein, a peptide, a peptidomemetic, an antibody,a ribozyme, a small molecule chemical compound, a nucleic acid, avector, and an antisense nucleic acid. In one embodiment, the disease ordisorder is cystic fibrosis.

In one aspect, the present invention provides a method for treating orpreventing a disease or disorder associated with degradation offunctional mutant protein in a subject in need thereof, where the methodcomprises administering to the subject a composition comprising amodulator of one or more TRIM proteins. In one embodiment, the modulatorincreases the expression or activity of the one or more TRIM proteins.In one embodiment, the modulator is at least one of the group consistingof a chemical compound, a protein, a peptide, a peptidomemetic, anantibody, a ribozyme, a small molecule chemical compound, a nucleicacid, a vector, and an antisense nucleic acid. In one embodiment, thedisease or disorder is cystic fibrosis.

In one aspect, the present invention provides a composition for treatingor preventing a disease or disorder associated with misfolded protein orprotein aggregates, where the composition comprises a modulator of oneor more SUMO-targeted ubiquitin ligase (STUbl). In one embodiment, themodulator increases the expression or activity of one or more STUbLs. Inone embodiment, the modulator is at least one of a chemical compound, aprotein, a peptide, a peptidomemetic, an antibody, a ribozyme, a smallmolecule chemical compound, a nucleic acid, a vector, and an antisensenucleic acid. In one embodiment, the modulator increases the expressionor activity of RNF4.

In one aspect, the present invention provides a method for treating orpreventing a disease or disorder associated with misfolded protein orprotein aggregates in a subject in need thereof, where the methodcomprises administering to the subject a composition comprising amodulator of one or more STUbLs. In one embodiment, the modulatorincreases the expression or activity of one or more STUbLs. In oneembodiment, the modulator is at least one of a chemical compound, aprotein, a peptide, a peptidomemetic, an antibody, a ribozyme, a smallmolecule chemical compound, a nucleic acid, a vector, and an antisensenucleic acid. In one embodiment, the modulator increases the expressionor activity of RNF4.

In one aspect, the present invention provides a method for producing arecombinant protein, where the method comprises administering amodulator of one or more TRIM proteins to cell modified to express arecombinant protein. In one embodiment, the modulator comprises anisolated peptide comprising one or more TRIM proteins. In oneembodiment, the modulator comprises an isolated nucleic acid moleculeencoding one or more TRIM proteins.

BRIEF DESCRIPTION OF THE DRAWINGS

The following detailed description of preferred embodiments of theinvention will be better understood when read in conjunction with theappended drawings. For the purpose of illustrating the invention, thereare shown in the drawings embodiments which are presently preferred. Itshould be understood, however, that the invention is not limited to theprecise arrangements and instrumentalities of the embodiments shown inthe drawings.

FIG. 1 , comprising FIG. 1A through FIG. 1L, depicts the results ofexample experiments demonstrating that PML promotes the degradation ofAtxn1 82Q and other nuclear misfolded proteins. (FIG. 1A) HeLa cellstransfected with Atxn1 82Q-GFP were stained with anti-PML antibody (red)and DAPI (blue). Individual and merged images are shown. Scale bar, 10μm. (FIG. 1B) Atxn1 82Q-GFP was expressed alone or together with PML inHeLa cells. Left, representative fluorescence images of cells. Scalebar, 20 μm. Right, quantification of cells based on sizes of Atxn182Q-GFP inclusions. (FIG. 1C) Atxn1 82Q-GFP was expressed alone ortogether with PML in HeLa cells (left), or alone in HeLa cells that werepreviously treated with control (−) or PML siRNA. Cell lysate fractions(when indicated) and whole-cell lysates (WCL) were analyzed by filterretardation assay (for SR fraction) or western blot (WB; for the rest).Molecular weight standards (in kDa) and relative ratios of SS or SRAtxn1 versus actin are indicated. (FIG. 1D) Steady-state levels ofFLAG-Atxn1 82Q or 30Q when expressed alone or together with PML in HeLacells (left), or when expressed alone in HeLa cells that were treatedwith control or PML siRNA (right), analyzed by WB. (FIG. 1E) Effect ofPML on the stability of total FLAG-Atxn1 82Q protein, analyzed by apulse-chase assay and autoradiography. The relative amounts of³⁵S-labeled Atxn1 82Q are indicated. (FIG. 1F and FIG. 1G) Effect of PMLoverexpression (FIG. 1F) and knockdown (FIG. 1G) on the stability ofAtxn1 82Q-GFP, analyzed by CHX treatment and WB. (FIG. 1H) Effect of PMLon Atxn1 82Q-GFP levels in the absence or presence of MG132. (FIG. 1I)Top, relative percentages of Httex1p 97QP-expressing cells withcytoplasmic (left) and nuclear (right) inclusions, in the absence orpresence of PML (means+SD, n=3). Bottom, representative fluorescenceimages of transfected cells immunostained with an anti-Htt antibody.Arrowheads indicate Httex1p 97QP aggregates. (FIG. 1J and FIG. 1K)Levels of HA-Httex1p 97QP and HA-Httex1p 97QP(KR) (FIG. 1J) andGFP-TDP-43 (FIG. 1K) in cells with and without PML overexpression.Virtually all Htt aggregates were in the SR fraction. (FIG. 1L)Stability of nFucDM-GFP in control and PML-depleted cells, analyzed byCHX treatment and WB.

FIG. 2 , comprising FIG. 2A through FIG. 2E, depicts the results ofexample experiments demonstrating the recognition of misfolded proteinsby PML. (FIG. 2A) Binding of GST-Htt 25Q and GST-Htt 103Q to immobilizedFLAG-PML and FLAG-GFP (negative control), analyzed by an in vitropull-down assay followed by WB (top and bottom) and Ponceau S staining(middle). *IgG heavy chain. (FIG. 2B) Binding of GST-PML (shown on theright) and the control GST protein to native (N) and urea-denatured (D)luciferase (luc) immobilized on Ni-NTA beads, analyzed as in (FIG. 2A).*Nonspecific proteins from BL21 bacterial lysates that bound to thecontrol beads. (FIG. 2C) Binding of indicated GST-Htt fusions toFLAG-PML CC conjugated on anti-Flag M2 beads or to control beads,analyzed by WB (top and middle) and Coomassie staining (bottom). (FIG.2D) Binding of PML F12/SRS2 (shown on the right) to a peptide libraryderived from luciferase. The N-terminal amino acid of the first peptideand the number of the last peptide spotted in each row are indicated.(FIG. 2E) The occurrence of each amino acid in PML SRS2-binding peptidesrelative to its occurrence in the luciferase peptide array (set at100%).

FIG. 3 , comprising FIG. 3A through FIG. 3F, depicts the results ofexample experiments demonstrating that SUMO2/3 is involved in theubiquitination and PML-mediated degradation of Atxn1 82Q. (FIG. 3A)SUMO1 and SUMO2/3 modification of Atxn1 82Q in HeLa cells treatedwithout or with MG132. For better comparison of modified Atxn1 82Q,Denaturing immunoprecipitation (d-IP) products with a similar level ofunmodified Atxn1 82Q were analyzed by WB. *Nonspecific bands. (FIG. 3B)Localization of Atxn1 82Q (detected by anti-FLAG antibody, red) inGFP-SUMO2- or GFP-SUMO3-expressing U2OS cells treated with or withoutMG132. Scale bar, 10 μm. (FIG. 3C) SUMO2/3 modification of Atxn1 82Q and30Q in HeLa cells, analyzed by d-IP followed by WB (top) and Ponceau Sstaining (bottom). (FIG. 3D) Atxn1 82Q was expressed alone or togetherwith SUMO1 or HA-SUMO2 KR in HeLa cells that were previously transfectedwith the indicated siRNA or un-transfected (−). Cells were treated withor without MG132. SUMOylation and ubiquitination of FLAG-Atxn1 82Q wasanalyzed by d-IP and WB. (FIG. 3E) Levels of Atxn1 82Q-GFP expressedalone or together with increasing amounts of PML in HeLa cellspretreated with the indicated siRNA. (FIG. 3F) Effect of PML on Atxn182Q-GFP levels in the presence or absence of SUMO1 or SUMO2 KR.

FIG. 4 , comprising FIG. 4A through FIG. 4F, depicts the results ofexample experiments demonstrating that PML promotes SUMOylation of Atxn182Q. (FIG. 4A) SUMOylation of FLAG-Atxn1 82Q in HeLa cells in theabsence or presence of HA-PML cells, and without or with MG132treatment. The amount of Atxn1 82Q DNA used for transfected was adjustedto yield comparable levels of the unmodified protein. (FIG. 4B and FIG.4C) SUMOylation of FLAG-Atxn1 82Q (FIG. 4B) and FLAG-nFlucDM-GFP (FIG.4C) in control and PML siRNA-transfected HeLa cells treated without orwith MG132. (FIG. 4D and FIG. 4E) SUMOylation of purified HA-Atxn182Q-FLAG was performed in the presence of recombinant FLAG-PML, FLAG-PMLM6, and SUMO2 as indicated. In (FIG. 4D), the amounts of different d-IPproducts were adjusted to yield a similar level of unmodified Atxn1 82Q(middle). (FIG. 4F) Levels of Atxn1 82Q-GFP in HeLa cells in the absenceor presence of increasing amounts of PML or PML M6.

FIG. 5 , comprising FIG. 5A through FIG. 5I, depicts the results ofexample experiments demonstrating a role of RNF4 in the degradation ofAtxn1 82Q. (FIG. 5A) Levels of Atxn1 82Q-GFP in HeLa cells without andwith RNF4 overexpression. (FIG. 5B and FIG. 5C) Effect of RNF4overexpression on Atxn1 82Q-GFP stability in control and PML-depletedHeLa cells, analyzed by CHX treatment and WB. Relative SS Atxn182Q/actin ratios are shown in (FIG. 5C). (FIG. 5D) Levels of FLAG-Atxn182Q in HeLa cells pretreated with a control siRNA (−) or a combinationof three RNF4 siRNAs. (FIG. 5E) Representative fluorescent images ofAtxn1 82Q-GFP in control and RNF4-knockdown HeLa cells. Scale bar, 20 μm(FIG. 5F) Localization of Atxn1 82Q-GFP and endogenous RNF4 in HeLacells treated with vehicle (DMSO) or MG132. Scale bar, 10 μm. (FIG. 5Gand FIG. 5H) Levels of FLAG-Atxn1 82Q and FLAG-Atxn1 30Q (FIG. 5G) orHA-Httex1p 97QP and HA-Httex1p 97QP(KR) (FIG. 5H) in HeLa cells withoutand with RNF4 overexpression. (FIG. 5I) Stability of nFlucDM-GFP in HeLacells stably expressing shCtrl and shRNF4 (left) and the levels of RNF4in these cells (right).

FIG. 6 , comprising FIG. 6A through FIG. 6I, depicts the results ofexample experiments demonstrating that RNF4 promotes the ubiquitinationand degradation of SUMO2/3-modified Atxn1 82Q. (FIG. 6A and FIG. 6B)Levels of SUMOylated FLAG-Atxn1 82Q (FIG. 6A) and FLAG-nFlucDM-GFP (FIG.6B), in the absence or presence of RNF4, in HeLa cells treated with orwithout MG132. d-IP products with similar levels of unmodified proteins,as well as WCL, were analyzed. (FIG. 6C) Levels of SUMOylated FLAG-Atxn182Q in HeLa cells that were pretreated with a control siRNA or acombination of RNF4 siRNAs, analyzed as in (FIG. 6A). (FIG. 6D and FIG.6E) Unmodified and SUMO2-modified FLAG-Atxn1 82Q proteins conjugated onM2 beads (+), or control M2 beads (−), were incubated withubiquitination reaction mixture, in the absence or presence of GST-RNF4.(FIG. 6D) A schematic diagram of the experimental design. (FIG. 6E) WBanalysis of FLAG-Atxn1 82Q (left) and GST-RNF4 (right). (FIG. 6F andFIG. 6G) Localization of Atxn1 82Q-GFP and RNF4 proteins (detected byanti-FLAG antibody) in HeLa. Scale bar, 10 μm. (FIG. 6H) Effect of theindicated RNF4 proteins on Atxn1 82Q-GFP levels in HeLa cells. (FIG. 6I)Effect of PML overexpression on Atxn1 82Q-GFP levels in HeLa cells thatwere pretreated with control or RNF4 siRNA.

FIG. 7 , comprising FIG. 7A through FIG. 7I, depicts the results ofexample experiments demonstrating that PML deficiency exacerbatesbehavioral and pathological phenotypes of the SCA1 mouse model. (FIG. 7Aand FIG. 7B) Retention times (average+SEM) on accelerating Rotarod at 7(FIG. 7A) and 11 (FIG. 7B) weeks of age, with the number of animalsindicated in parenthesis. (FIG. 7C and FIG. 7D) Cerebellar sections of12-week-old animals were stained with hematoxylin. (FIG. 7C)Quantification of molecular layer thickness (means±SEM, n=3mice/genotype). (FIG. 7D) Representative images of the staining. Scalebar, 200 μm. (FIG. 7E and FIG. 7F) Cerebellar sections of 1-year-oldanimals were stained with an anti-calbindin antibody. (E) Quantitationof Purkinje cells, graphed as the average number of soma per 1 mm length(means±SEM, n=4 mice/genotype). (F) Representative images of thestaining. Scale bar, 200 μm. (FIG. 7G and FIG. 7H) Sections of thecerebellar cortex from 12-week-old mice were stained with ananti-ubiquitin antibody and counterstained with hematoxylin. (FIG. 7G)Percentage of Purkinje cells with aggregates (means SEM, n=3mice/genotype). (FIG. 7H) Representative images of theimmunohistochemistry staining. Arrowheads indicate the ubiquitinpositive aggregates in Purkinje cell bodies. Scale bar, 50 μm. Noubiquitin-positive aggregates were observed in Purkinje cells in micewithout Atxn1^(tg/−) (see FIG. 14D). (FIG. 7I) A model for PQC by thePML-RNF4 system. PML recognizes misfolded proteins through SRSs andconjugates them with poly-SUMO2/3 chain through its SUMO E3 ligaseactivity (a). RNF4 ubiquitinates SUMOylated-misfolded proteins (b) andtargets them for proteasomal degradation (c).

FIG. 8 , comprising FIG. 8A through FIG. 8G, depicts the results ofexample experiments demonstrating that PML co-localizes with Atxn1 82Qaggregates and decreases insoluble Atxn1 82Q. (FIG. 8A) Atxn1 82Q-GFPwas expressed in PML-deficient (PML^(−/−)) mouse embryonic fibroblasts(MEFs) together with each of the indicated PML isoforms. Cells werestained with anti-PML antibody (red) and DAPI (blue). (FIG. 8B) Levelsof FLAG-Atxn1 82Q in HeLa cells treated with a control siRNA (−), PMLsiRNA #4, or PML siRNA #9. Cell lysates were analyzed by Western blotand filter retardation assays. The ratios of Atxn1 82Q in the SSfraction versus actin, normalized to the control, are shown. (FIG. 8C)HeLa cells were transfected with a control siRNA, PML siRNA #4 (whichtargeted the 5′UTR of the PML mRNA), or PML siRNA #4 plus a plasmidexpressing the open reading frame of PML (hence resistant to the siRNA).Levels of Atxn1 82Q-GFP in various fractions were analyzed. (FIG. 8D)HeLa cells were treated with control siRNA, PML siRNA #4, and PML siRNA#9 and then transfected with FLAG-Atxn1 82Q. The levels of theFLAG-Atxn1 82Q transcript were determined by quantitative RT-PCRnormalized to levels of 18S rRNA. (FIG. 8E) Atxn1 30Q-GFP was expressedin HeLa cells in the absence or presence of PML. Cells were then treatedwith CHX for the indicated times. (FIG. 8F) HeLa cells were transfectedwith nFlucDM-GFP and the corresponding wild-type luciferase (WT)protein. Endogenous PML was detected by an anti-PML antibody (red), andDNA by DAPI (blue). Scale bar: 10 μm. (FIG. 8G) PML knockdown leads toaccumulation of insoluble mutant luciferase. HeLa cells were transfectedwith control or PML siRNA and then with nFluc-GFP or nFlucDM-GFP. The SRfraction contained very small amounts of nFlucDM-GFP.

FIG. 9 , comprising FIG. 9A through FIG. 9E, depicts the results ofexample experiments demonstrating the interaction of PML with pathogenicHtt proteins. (FIG. 9A) PML preferentially interact with pathogenic Htt.Lysates of 293T cells expressing FLAG-GFP or FLAG-PML were incubatedwith GST-Htt 25Q or GST-Htt 103Q immobilized on glutathione beads (lanes1-3 and 5-7), or with control glutathione beads (lanes 4 and 8). Theinput and pull-down fractions were analyzed by Western blot. (FIG. 9B)Schematic representation of wild-type PML isoforms IV (aa 1-633) (calledPML in the present work) and various deletion fragments (F1-F10). TheRING domain (R), B1 box, B2 box, and coiled-coil region (CC) arelabeled. Substrate recognition sites SRS1 and SRS2 are indicated bylines. The interaction of PML with pathogenic Htt proteins (Htt 103Q or52Q) and denatured luciferase are shown. ND: not done. (FIG. 9C)Interactions of full-length PML and PML deletion mutants with Htt. PMLproteins were generated by coupled in vitro transcription/translation inthe presence of [35S]Met, and were incubated with purified GST-Htt 103Q,GST-Htt 25Q, or GST immobilized on glutathione beads. [³⁵S]Met-labeledproteins in the input and pull-down samples were analyzed byautoradiography, and GST proteins in the pull-down samples were analyzedby Coomassie staining. The three pull-down sample sets were analyzed atthe same time and in the same way, including the amount of samples andthe exposure duration of autoradiography. The input samples were exposedfor a shorter period of time. (FIG. 9D) Sequences of Htt 52Q and theCC-destabilizing (cc-) mutant. The amino acids in Htt 52Q that arechanged to Pro in Htt 52Q cc- are shown in red. (FIG. 9E) Interaction ofpurified PML CC region (shown on the right) with cellulose-boundluciferase peptide scans was assayed as in FIG. 2D. * TEV protease.

FIG. 10 , comprising FIG. 10A through FIG. 10C, depicts the results ofexample experiments demonstrating the interaction of PML with denaturedluciferase. (FIG. 10A) Interaction of PML fragments with denaturedluciferase. In vitro-translated, [¹⁵S]-labeled full-length FLAG-PML andFLAG-PML deletion mutants were incubated with native or denaturedluciferase immobilized on beads, or control beads. The input andbeads-bound PML proteins were analyzed by autoradiography, andluciferase by Coomassie blue staining. *, Non-specific bands. The threepull down sample sets were analyzed at the same time and in the sameway, including the amount of samples and the exposure duration ofautoradiography. The input samples were exposed for a shorter period oftime. (FIG. 10B and FIG. 10C) Identification of the second substraterecognition site (SRS2) on PML. (FIG. 10B) PML deletion mutationsencompassing amino acids at the C-terminus and summary of theirinteraction with denatured luciferase. (FIG. 10C) In vitro-translated,[³⁵S]-labeled GST-fusions of PML fragments or GST were tested forinteraction with luciferase as described in (FIG. 10A).

FIG. 11 , comprising FIG. 11A through FIG. 11G, depicts the results ofexample experiments demonstrating the modification of misfolded proteinsby SUMO2/3. (FIG. 11A) HeLa cells were transfected with FLAG-Atxn1 82Qor FLAG-Atxn1 82Q (5KR) and were treated with or without MG132.FLAG-Atxn1 82Q and FLAG-Atxn1 82Q (5KR) were isolated by d-IP, and theirSUMO2/3 modification was analyzed by Western blot. (FIG. 11B) HeLa cellswere transfected without or with GFP-TDP-43 and treated with vehicle(DMSO) (−) or MG132 (+). d-IP was performed using an anti-GFP antibodyor a control antibody. d-IP products were analyzed by Western blot.(FIG. 11C) HeLa cells were transfected with nFluc-GFP, nFlucSM-GFP, andnFlucSM-GFP (each was also N-terminally tagged with the FLAG epitope)and treated with or without MG132. nFluc proteins were isolated by d-IP.The whole cell lysates (WCL) and IP products were analyzed by Westernblot. Note that the difference between the SUMO2/3 modifications of WTluciferase versus SM/DM luciferase (top, lanes 1-3) was not due to achange in the overall SUMO2/3 conjugation in the WCL (bottom). (FIG.11D) Atxn1 82Q-GFP was expressed in HeLa cells pre-treated with control(Ctrl), SUMO2/3, or SUMO1 siRNA. Cell lysates were analyzed by Westernblot. (FIG. 11E and FIG. 11F) HeLa cells were treated with control(Ctrl) siRNA, SUMO2/3 siRNA, or SUMO1 siRNA (FIG. 11E), or treated withthese siRNAs and then transfected with GFP (FIG. 11F). Cell lysates wereanalyzed by Western blot. (FIG. 11G) PML and PML M6 proteins used for invitro SUMOylation assay. FLAG-PML and FLAG-PML M6 were expressed in 293Tcells and purified by anti-FLAG (M2) beads. The proteins were analyzedby Coomassie staining along with BSA standards (left) and by Westernblot (right). The two additional bands (arrowheads) presented in bothPML and PML M6 lanes (left) were determined to be PML fragments based onboth Western blot (right) and by mass spectrometry analysis. A schematicrepresentation of M6 mutant is shown at the bottom. *: Point mutationsare described elsewhere herein.

FIG. 12 , comprising FIG. 12A through FIG. 12I, depicts the results ofexample experiments demonstrating that RNF4 promotes degradation ofmisfolded proteins. (FIG. 12A) Representative fluorescence images ofHeLa cells expressing Atxn1 82Q-GFP alone or together with RNF4. Scalebar: 20 μm. Images are from the same experiment as that shown in FIG.1B. (FIG. 12B) The half-life of Atxn1 82Q-GFP in HeLa cells with andwithout RNF4 overexpression. Samples are from the same experiments asthose shown in FIG. 1F. (FIG. 12C) HeLa cells were transfected withcontrol siRNA (−), RNF4 siRNA alone, or RNF4 siRNA plus ansiRNA-resistant RNF4. Cell lysates were analyzed by Western blot. (FIG.12D) FLAG-Atxn1 82Q was expressed in HeLa cells that were pre-treatedwith control siRNA and the indicated RNF4 siRNA. FLAG-Atxn1 82Q wasisolated by d-IP with anti-FLAG M2 beads. WCL and IP products wereanalyzed by Western blot with indicated antibodies. (FIG. 12E) HeLacells expressing both Atxn1 82Q-GFP and FLAG-RNF4 were treated withvehicle (DMSO) or MG132. Exogenous (Exo.) RNF4 was detected anti-FLAGantibody. In control cells treated with DMSO, exogenous RNF4 showedpartial co-localization with Atxn1 82Q-GFP aggregates. Upon MG132treatment, complete co-localization of exogenous RNF4 with Atxn1 82Qaggregates was observed in 100% of cells. Scale bar: 10 μm. (FIG. 12F)Western blot analysis of HeLa cells transfected with GFP-TDP-43 alone ortogether with increasing amounts of RNF4. (FIG. 12G) GFP-TDP-43 wasexpressed in cells pre-treated with a control siRNA (−) or the indicatedRNF4 siRNA. 500 cells were counted in each experiment. Percentages ofcells with GFP-TDP-43 foci are shown. (FIG. 12H) HeLa cells treated withRNF4 siRNA were transfected with GFP-TDP-43. Cells were stained with ananti-RNF4 antibody (red) and DAPI (blue). Note that TDP-43 formedaggregates in a cell in which RNF4 was knocked down (filled arrowhead),but was diffused in a control cell (open arrowhead). (FIG. 12I) HeLacells were transfected with GFP-TDP-43 and treated with MG132.Endogenous RNF4 was immunostained with anti-RNF4 antibody (red). Notethat RNF4 also formed nuclear foci in cells with no TDP-43 (FIG.12E-FIG. 12H).

FIG. 13 , comprising FIG. 13A through FIG. 13F, depicts the results ofexample experiments demonstrating that SUMO2/3 are involved inRNF4-mediated degradation of Atxn1 82Q. (FIG. 13A) Atxn1 82Q-GFP and/orRNF4 were expressed in HeLa cells pre-treated with control siRNA,SUMO2/3 siRNA, and SUMO1 siRNA. Cell lysates were analyzed by Westernblot. (FIG. 13B) U20S cells stably expressing GFP-SUMO2 were transfectedfirst with the indicated RNF4 siRNAs or a control siRNA (−) and thenwith FLAG-Atxn1 82Q. The percentages of transfected cells withGFP-SUMO2-positive Atxn1 82Q aggregates are shown (mean+SD, n=3). Ineach experiment, 200 cells were counted. Representative images of thetransfected cells are shown on the right. GFP-SUMO2 does not formaggregated structure in cells without Atxn1 82Q expression. (FIG. 13C)Schematic representation of wild-type and mutant RNF4 proteins. TheSUMO-interaction motifs (SIMs) 1 to 4 and the RING domain are shown. *:Point mutations are described elsewhere herein. (FIG. 13D and FIG. 13E)Purified recombinant GST fusions of rat (r) RNF4 and RNF4 CS1 (FIG. 13D)or human RNF4 and RNF4 SIMm (FIG. 13E) were incubated with ubiquitin E1,E2 (UbcH5a), and ubiquitin (Ub) as indicated, plus Mg²⁺-ATP. Thereaction mixtures were analyzed by Western blot using an anti-GSTantibody. (FIG. 13F) Expression of Atxn1 82Q-GFP in cells treated withthe indicated combinations of control, PML, and RNF4 siRNAs asindicated. Cell lysates were analyzed by Western blot.

FIG. 14 , comprising FIG. 14A through FIG. 14D, depicts the results ofexperiments demonstrating that PML deficiency reduces arborization ofPurkinje cell dendrites but does not result in aggregates in Purkinjecells. (FIG. 14A) Midsagittal cerebellar sections of 12-week-old micewere stained with an antibody against the Purkinje cell-specific proteincalbindin. Fluorescence intensity was plotted from a rectangular areafrom the preculminate fissures (n=2 mice for PML^(+/+), and n=3 mice forall the other genotypes). PML^(−/−) mice showed significant loss ofdendritic arborization compared to PML^(+/+) mice (ANOVA, p=0.031).(FIG. 14B) Representative confocal images of calbindinimmunofluorescence. Scale bar: 100 μm. (FIG. 14C) Quantitation ofPurkinje cell density in 12-week PML^(+/+), PML^(+/−) and PML^(−/−) micewith and without Atxn1^(tg/−), graphed as the average number of soma per1 mm length (means+SEM, n=3 mice/genotype). (FIG. 14D)Immunohistochemical staining of the cerebellar cortex sections from12-week-old PML^(+/+) and PML^(−/−) mice without Atxn1^(tg/−). Thesections were stained with an anti-ubiquitin antibody and counterstainedwith hematoxylin. Scale bar: 50 μm. Note that no ubiquitin positiveaggregates were detected in those sections. The stained sections ofPML^(+/+):Atxn1^(tg/−) and PML^(−/−):Atxn1^(tg/−) mice are shown in FIG.7G.

FIG. 15 , comprising FIG. 15A through FIG. 15D, depicts the results ofexample experiments demonstrating the co-localization of TRIM27, TRIM32,and TRIM5δ with EGFP-Atxn1 82Q and Httex1p 97QP. (FIG. 15A) Atxn182Q-GFP was expressed in HeLa cells together with the indicatedFLAG-tagged TRIM proteins. Cells were stained with anti-FLAG antibody(red) and DAPI (blue). Scale bar: 10 μm. (FIG. 15B and FIG. 15C) Httex1p97QP was expressed in HeLa cells together with FLAG-tagged TRIM5δ,TRIM27 (FIG. 15B), and TRIM32 (FIG. 15C). Cells were immunostained withanti-huntingtin (green) and anti-FLAG (red) antibodies. Note that TRIM32co-localized with Httex1p 97QP regardless of the cellular localizationof Httex1p 97QP. (FIG. 15D) HeLa cells were transfected with Atxn182Q-GFP. Endogenous TRIM27 was detected by anti-TRIM27 antibody (red).Arrowheads indicate endogenous TRIM27 bodies that were co-localized withthe Atxn1 82Q aggregates. Scale bar: 10 μm.

FIG. 16 , comprising FIG. 16A through FIG. 16D, depicts the results ofexample experiments demonstrating the reduction of aggregated Atxn1 82Qby TRIM27, TRIM32, and TRIM5δ. (FIG. 16A and FIG. 16B) Levels of Atxn182Q-GFP when expressed alone (−) or together with the indicatedFLAG-tagged TRIM proteins in HeLa cells. The cell lysates were analyzedby Western blot. In the left panel of (FIG. 16A), the ratios of Atxn182Q in the SS fraction versus actin are given, and the expression ofTRIM11 could be detected after a prolonged exposure. (FIG. 16C)Expression levels of Atxn1 82Q in HeLa cells treated with control (−) orTRIM27 siRNA. *, a non-specific band. (FIG. 16D) PIASy does not inhibitthe levels of Atxn1 82Q protein. Western blot analysis of HeLa cellstransfected with Atxn1 82Q-GFP, PIASy, and PML as indicated.

FIG. 17 , comprising FIG. 17A through FIG. 17C, depicts the results ofexample experiments demonstrating that TRIM27 and TRIM32 reduceaggregated Atxn1 82Q independent of PML. (FIG. 17A) Partialco-localization of TRIM27 with PML. HeLa cells transfected withFLAG-TRIM27 were immunostained with anti-FLAG (green) and anti-PML (red)antibodies. (FIG. 17B) Co-localization of TRIM27 with Atxn1 82Q-GFPaggregates in PML^(+/+) and PML^(−/−) MEFs. FLAG-TRIM 27 was stained byanti-FLAG (red) antibody. (FIG. 17C) Atxn1 82Q-GFP was expressed aloneor together with the indicated TRIM proteins in PML^(+/−) and PML^(−/−)MEFs. Extracts were analyzed by filter retardation assay. To bettercompare the effects of TRIM proteins on the aggregates, a lighterexposure is shown on the right panel.

FIG. 18 , comprising FIG. 18A through FIG. 18G, depicts the results ofexample experiments demonstrating that TRIM proteins depend on SUMO2/3and the proteasome to remove insoluble Atxn1 82Q. (FIG. 18A-FIG. 18F)Atxn1 82Q-GFP was expressed alone or together with TRIM5δ, TRIM27, andTRIM32 in cells treated without or with MG132 (FIG. 18A-FIG. 18C), or incontrol or SUMO2/3 knockdown cells (FIG. 18D-FIG. 18F). Cell lysateswere analyzed by Western blot. (FIG. 18G) SUMOylation of purifiedHA-Atxn1 82Q-FLAG was performed in the presence of recombinantFLAG-TRIM11 and SUMO2 as indicated. HA-Atxn1 82Q-FLAG was isolated usingdenaturing immunoprecipitation. The reaction mixtures and IP sampleswere analyzed by Western blot.

FIGS. 19 , comprising FIG. 19A through FIG. 19D, depicts the results ofexample experiments demonstrating the localization of TRIM proteins inrelation to Atxn1 82Q. Atxn1 82Q-GFP (green) was expressed in HeLa cellstogether with the indicated HA-tagged TRIM proteins. Cells wereimmunostained with anti-HA antibody (red). The representativelocalization patterns for each TRIM protein are shown. (FIG. 19A) Therepresentative localization patterns of TRIM1-TRIM 16. (FIG. 19B) Therepresentative localization patterns of TRIM17-TRIM32. (FIG. 19C) Therepresentative localization patterns of TRIM33-TRIM41 and TRIM44-TRIM41. (FIG. 19D) The representative localization patterns of TRIM52,TRIM54-TRIM58, TRIM62-TRIM66, TRIM73-TRIM74, and TRIM76. TRIM proteinsthat showed co-localization with Atxn1 82Q-GFP in a substantial numberof cells are indicated in yellow. Scale bar: 10 μm.

FIG. 20 , comprising FIG. 20A and FIG. 20B, depicts the results of asystematic analysis of TRIM proteins on Atxn1 82Q and Httex1p 97QP.Atxn1 82Q-GFP (FIG. 20A) or Httex1p 97QP (FIG. 20B) was co-expressedwith the indicated TRIM proteins in HeLa cells. Cell lysates wereanalyzed by Western blot. TRIM proteins labeled red and green are thosethat reduced and increased the levels of the polyQ proteins,respectively, while TRIM proteins labeled in black had no observableeffect. Note that the effects of TRIM proteins can be influenced bytheir levels of expression, as described elsewhere herein.

FIG. 21 , comprising FIG. 21A through FIG. 21C, depicts the results ofexample experiments demonstrating that recombinant TAT-TRIM11 reducesthe levels of misfolded proteins. HeLa cells were transfected with Atxn182Q-GFP, Atxn1 30Q, or Htt 97Q-GFP, and were subsequently incubated withrecombinant TRIM11 or SUMO2 proteins. (FIG. 21A) Treatment of HeLa cellswith TRIM11 led to strong reduction in the levels of Atxn1 82Q. (FIG.21B) Treatment of HeLa cells with TRIM11 also led to strong reduction inthe levels of Htt 97Q. (FIG. 21C) SUMO2 had minimal effect on the levelsof Atxn1 82Q.

FIG. 22 depicts the amino acid sequence of Tat-TRIM11 used in exampleexperiments.

FIG. 23 , comprising FIG. 23A through FIG. 23F, depicts results ofexperiments demonstrating RNF4 staining of human brain samples.Anti-RNF4 (green) immunostaining of HD brain tissues. RNF4 showeddiffused nuclear localization (FIG. 23A-FIG. 23C) or formed foci (FIG.23D-FIG. 23F) (indicated by arrowheads). Scale bar: 10 μm.

FIG. 24 , comprising FIG. 24A through FIG. 24H, depicts results ofexperiments demonstrating co-localization of RNF4 with neuronalinclusions of SCA1 patients. Immunostaining of SCA1 brain tissues withanti-polyQ (1C2) and anti-RNF4 antibodies. Scale bar: 10 μm.

FIG. 25 , comprising FIG. 25A through FIG. 25L, depicts results ofexperiments demonstrating co-localization of RNF4 with neuronalinclusions of SCA1 patients. FIG. 25 depicts immunostaining of HD braintissues with anti-Htt, anti-ubiquitin and two separate RNF4 antibodies.Note that Htt and ubiquitin form ring-like structures (FIG. 25A-FIG.25H) or evenly distributed inclusions (FIG. 25I-FIG. 25L) with the RNF4signal in the center.

FIG. 26 , comprising FIG. 26A through FIG. 26H, depicts results ofexperiments demonstrating co-localization of RNF4 with inclusions inneurons of HD patients. Shown are Htt and RNF4 immunostaining of HDbrain tissues. Two different RNF4 antibodies (#1 and #2) were used.Scale bar: 10 μm.

FIG. 27 , comprising FIG. 27A through FIG. 27D, depicts results fromexperiments demonstrating SUMOylation of Atxn1 82Q, p53 andalpha-Synuclein. FIG. 27A depicts experiments where SUMOylation of Atxn182Q was analyzed when TRIM11 WT, TRIM11 MUT or PML was co-expressed.Before lysis, 10 μM MG132 was added for 4 hours. FIG. 27B depicts invitro SUMOylation of purified Atxn1 82Q incubated with TRIM11 WT orTRIM11 MUT in the presence of E1, E2 and SUMO2. FIG. 27C depicts invitro SUMOylation of purified Flag-p53 incubated with TRIM11 or PML inthe presence of E1, E2 and SUMO2. FIG. 27D depicts in vitro SUMOylationof alpha-Synuclein incubated with TRIM11 WT in the presence or absenceof E1, E2 and SUMO2.

FIG. 28 , comprising FIG. 28A through FIG. 28G, depicts results fromexperiments demonstrating TRIM11 is recruited to Atxn1 82Q aggregates.FIG. 28A depicts immunofluorescence analysis of transfected GFP-Hsp70 in293T cells. FIG. 28B depicts immunofluorescence analysis of transfectedGFP-TRIM11 in 293T cells. FIG. 28C depicts immunofluorescence analysisshowing that Hsp70 can be recruited into the aggregates of Atxn1 82Q.FIG. 28D depicts immunofluorescence analysis showing that TRIM11 can berecruited into the aggregates of Atxn1 82Q. FIG. 28E depictsimmunoblotting analysis detergent-soluble and insoluble fractions ofcells transfected with Atxn1 82Q, TRIM11 or Hsp70. Where indicated, 10μM MG132 is added for 3 hours. FIG. 28F depicts immunoblotting analysisof detergent-soluble and insoluble fractions of cells transfected withAtxn1 82Q, TRIM11 WT (wild type) or TRIM11 MUT (mutation). Whereindicated, 10 μM MG132 is added for 3 hours. FIG. 28G depictsimmunoblotting where HCT116 cells are transfected with the indicatedplasmids. After 48 hours, cells were lysed and then stained with 20 μMThioflavin-T (ThT).

FIG. 29 , comprising FIG. 29A through FIG. 29C, depicts results fromexperiments demonstrating TRIM11 binding to Atxn1 82Q. FIG. 29A depictspurified experiments where Flag-Atxn1 82Q immobilized on beads wasincubated with GST or GST-TRIM11. FIG. 29B experiments where depictspurified Flag-Atxn1 82Q or Flag-Atxn1 30Q immobilized on beads wasincubated with GST or GST-TRIM11. FIG. 29C depicts binding of GST-TRIM11and GST protein to native (N) and urea-denatured (D) luciferase (luc)immobilized on Ni-NTA beads.

FIG. 30 , comprising FIG. 30A through FIG. 30D, depicts results fromexperiments demonstrating TRIM11 reduces cellular aggregates. FIG. 30Adepicts experiments where HCT116 cells stably expressing GFP-Atxn1 82Qwere lysed and then stained with 20 μM Thioflavin-T (ThT). FIG. 30Bdepicts sedimentation analysis of GFP-Atxn1 82Q-HCT116 cells transfectedwith TRIM11. FIG. 30C depicts experiments where HCT116 cells stablyexpressing GFP-Atxn1 82Q were transfected with TRIM11 WT or TRIM11 MUT.After 48 hours, cells were lysed and stained with 20 μM ThT. FIG. 30Ddepicts sedimentation analysis of GFP-Atxn1 82Q-HCT116 cells transfectedwith TRIM11 WT or TRIM11 MUT.

FIG. 31 , comprising FIG. 31A through FIG. 31H, depicts results fromexperiments demonstrating TRIM11 acts as a molecular chaperone toprevent aggregate formation. FIG. 31A depicts experiments whereluciferase (10 nM) was incubated with 200 nM GST, 200 nM GST-TRIM11 or200 nM Hsp70 at 45° C. with the indicated time. Native luciferaseactivity was set as 100%. N=3. FIG. 31B depicts experiments where GFP(0.45 uM) was incubated with 200 nM GST, 200 nM GST-TRIM11 or 200 nMHsp70 at 45° C. with the indicated time. Native GFP fluorescence was setas 100%. N=3. FIG. 31C depicts the activity of transfected luciferase inHCT116 measured without heat shock as control. After 30 min heat shockat 45° C. or after 3 hour recovery at incubator, the luciferaseactivities were relative to the control. FIG. 31D depicts the activityof transfected luciferase in HCT116 measured without heat shock ascontrol. After 60 min heat shock at 45° C. or after 1.5 hour or 3 hourrecovery at incubator, the luciferase activities were relative to thecontrol. FIG. 31E depicts immunoblotting analysis of HCT116 cells stablyexpressing control vector or Flag-TRIM11. FIG. 31F depicts ThT analysisshowing the prevention of beta-amyloid fibrils formation by GST, TRIM11or Hsp70. FIG. 31G depicts a sedimentation assay showing the preventionof Atxn1 82Q aggregates formation by Lysozyme, GST or TRIM11. Theresults were shown by immunoblotting and dot-blot assay. FIG. 31Hdepicts a sedimentation assay showing the prevention of p53 aggregatesformation by L TRIM11. Where indicated, E1, E2, SUMO2 or ATP wasapplied. The results were shown by immunoblotting and dot-blot assay.

FIG. 32 , comprising FIG. 32A through FIG. 32G, depicts results fromexperiments demonstrating HSF1 is not required for regulating thetranscription of TRIM11. FIG. 32A depicts experiments where HCT116 cellswere treated with or without heat shock (42° C.) for 1 hour and thenrecovered for different time. Total cell lysates were subjected toimmunoblotting with the indicated antibodies. FIG. 32B depictsexperiments where HCT116 cells stably expressing Flag-TRIM11 weretreated with or without heat shock (42° C.) for 1 hour and thenrecovered for different time. Total cell lysates were subjected toimmunoblotting with the indicated antibodies. FIG. 32C depictsexperiments where HeLa cells were treated with or without heat shock(42° C.) for 1 hour and then recovered for different time. Total celllysates were subjected to immunoblotting with the indicated antibodies.FIG. 32D depicts experiments where A549 cells were treated with orwithout As₂O₃ for 30 min and then recovered for different time. Totalcell lysates were subjected to immunoblotting with the indicatedantibodies. FIG. 32E depicts experiments where A549 cells were treatedwith or without H₂O₂ for 100 min and then recovered for different time.Total cell lysates were subjected to immunoblotting with the indicatedantibodies. FIG. 32F depicts semi-quantitative PCR analysis of TRIM11,HSP70, HSP90 and GAPDH in response to heat shock. FIG. 32G depictsexperiments where A549 cells stably expressing vector or HSF1 weretreated with or without heat shock and recovered for 3 hours.Immunoblotting and semi-quantitative PCR were analyzed.

FIG. 33 , comprising FIG. 33A through FIG. 33F, depicts results fromexperiments demonstrating that p53 is a factor in upregulating TRIM11 inheat shock response. FIG. 33A depicts immunoblotting of HCT116 p53 wildtype or p53 null cells treated with heat shock and recovered. FIG. 33Bdepicts qPCR analysis of TRIM11 mRNA level in HCT116 p53 wild type orp53 null cells treated with heat shock and recovered. FIG. 33C depictsimmunoblotting and semi-quantitative PCR analysis of A549 cells stablyexpressing control (Ctrl) or p53 shRNA treated with or without heatshock and recovered for 3 hours. FIG. 33D depicts immunoblotting andsemi-quantitative PCR analysis of HCT116 cells transfected with Ctrl orp53 siRNA treated with or without heat shock and recovered for 3 hours.FIG. 33E depicts crystal violet analysis of survival of HCT116 cellswhich were heated and recovered for 24 hours. Where indicated, KRIBB11was added. FIG. 33F depicts relative cell numbers of results presentedin FIG. 33E analyzed by OD490.

FIG. 34 , comprising FIG. 34A through FIG. 34G, depicts results fromexperiments demonstrating TRIM11 acts as a disaggregase to resolvepreformed aggregates. FIG. 34A depicts disaggregation and reactivationof preformed luciferase aggregates using increasing concentrations ofLysozyme, GST or GST-TRIM11 (n=3). FIG. 34B depicts a sedimentationassay showing that heat-aggregated luciferase resolved by GST orGST-TRIM11. The results were shown by immunoblotting. FIG. 34C depictsdisaggregation and reactivation of preformed GFP aggregates usingincreasing concentrations of Lysozyme, GST or GST-TRIM11 (n=3). FIG. 34Ddepicts a sedimentation assay showing that heat-aggregated GFP resolvedby GST or GST-TRIM11. The results were shown by immunoblotting. FIG. 34Edepicts a sedimentation assay showing preformed Atxn1 82Q aggregatesresolved by Lysozyme, GST or TRIM11. The results were shown byimmunoblotting. FIG. 34F depicts a sedimentation assay showing thatpreformed Atxn1 82Q aggregates (left) and p53 aggregates (right)disaggregated by 1 μM Hsp70 and 0.5 μM Hsp40. FIG. 34G depicts asedimentation assay showing that preformed Atxn1 82Q aggregatesdisaggregated by 0.5 μM GST, 0.5 μM TRIM11, 1 μM Hsp70, 0.5 μM Hsp40 or1 μM Hsp104.

FIG. 35 , comprising FIG. 35A through FIG. 35D, depicts results fromexperiments demonstrating full length TRIM11 is required for refoldingactivity. FIG. 35A depicts a schematic diagram of TRIM11 structure. FIG.35B depicts disaggregation and reactivation of preformed luciferaseaggregates using increasing concentrations of the indicated proteins(n=3). FIG. 35C depicts a sedimentation assay showing heated luciferaseaggregates disaggregated by GST, TRIM11, RBC or B30.2. FIG. 35D depictsdisaggregation and reactivation of preformed luciferase aggregates usingthe indicated proteins (n=3).

FIG. 36 , comprising FIG. 36A and FIG. 36B depicts results fromexperiments demonstrating TRIM 11 binding to substrates is required forTRIM11 disaggregation function. FIG. 36A depicts purified Flag-Atxn1 82Qimmobilized on beads was incubated with GST, GST-TRIM11, GST-RBC orGST-B30.2. FIG. 36B depicts purified Flag-Atxn1 82Q immobilized on beadswas incubated with GST, GST-TRIM11 or other TRIM11 fragments.

FIG. 37 , comprising FIG. 37A through FIG. 37E depicts results fromexperiments demonstrating TRIM11 performs disaggregation independentlyof its SUMO E3 ligase activity. FIG. 37A depicts experiments whereluciferase (10 nM) was incubated with 200 nM GST, 200 nM GST-TRIM11 WTor MUT at 45° C. with the indicated time. Native luciferase activity wasset as 100%. N=3. FIG. 37B depicts disaggregation and reactivation ofpreformed luciferase aggregates by 200 nM GST, 200 nM GST-TRIM11 WT orMUT. FIG. 37C depicts the binding of GST, GST-TRIM11 WT or MUT to native(N) and urea-denatured (D) luciferase (luc) immobilized on Ni-NTA beads.FIG. 37D depicts immunofluorescence analysis of transfected GFP-TRIM11MUT in 293T cells. FIG. 37E depicts immunofluorescence analysis showthat TRIM11 MUT can be recruited into the aggregates of Atxn1 82Q.

FIG. 38 , comprising FIG. 38A through FIG. 38E, depicts results fromexperiments demonstrating TRIM11 can also preform alpha-Synucleinamyloid fibril formation and disaggregate preformed alpha-Synucleinfibers. FIG. 38A depicts ThT analysis showing prevention of alpha-Synfibrils formation by GST, TRIM11, Hsp70, Hsp40 or Hsp104. FIG. 38Bdepicts ThT analysis showing prevention of alpha-Syn fibrils formationby TRIM11 in a dose-dependent manner. FIG. 38C depicts EM images of thefiber formation of alpha-Syn monomer incubated with GST or GST-TRIM11.FIG. 38D depicts a sedimentation assay showing that preformed alpha-Synfiber disaggregated by TRIM11 and Hsp104 A503S. FIG. 38E depicts ThTanalysis showing disaggregation of preformed alpha-Syn fibrils by GST,TRIM11 or Hsp104.

FIG. 39 , comprising FIG. 39A through FIG. 39D, depicts results fromexperiments demonstrating TRIM21 has similar disaggregation functions toTRIM11. FIG. 39A depicts binding of GST, GST-TRIM11 WT or MUT to native(N) and urea-denatured (D) luciferase (luc) immobilized on Ni-NTA beads.FIG. 39B depicts a sedimentation assay showing that heat-aggregatedluciferase resolved by GST or GST-TRIM21. FIG. 39C depictsDisaggregation and reactivation of preformed luciferase aggregates usingincreasing concentrations of GST or GST-TRIM21 (n=3). FIG. 39D depicts aluciferase assay where luciferase (10 nM) was incubated with 200 nM GSTor 200 nM GST-TRIM21 at 45° C. for 1 min. Native luciferase activity wasset as 100%. N=3.

FIG. 40 , comprising FIG. 40A through FIG. 40E, depicts results fromexperiments demonstrating PML and Atxn1 82Q disaggregation. FIG. 40Adepicts commassie blue staining of purified Flag-PML6 from 293T cells.FIG. 40B depicts disaggregation and reactivation of preformed GFPaggregates using increasing concentrations of Lysozyme or Flag-PML6(n=3). FIG. 40C depicts disaggregation and reactivation of preformed GFPaggregates using Lysozyme, Flag-PML6 or GST-TRIM11 (n=3). FIG. 40Ddepicts commassie blue staining of purified Flag-PML4 fragments from293T cells. FIG. 40E depicts disaggregation and reactivation ofpreformed GFP aggregates using different PML4 fragments (n=3).

FIG. 41 , comprising FIG. 41A and FIG. 41B, depicts results fromexperiments demonstrating TRIM 11 in mouse primary hippocampal neurons.FIG. 41A depicts MTT analysis showing that GST or TRIM11 incubatedalpha-Syn-induced cell death. FIG. 41B depicts immunofluorescenceanalysis of p-alpha-Syn or p62 in alpha-Syn fiber treated Hippocampalneuron cells.

FIG. 42 , comprising FIG. 42A through FIG. 42C, depicts results fromexperiments demonstrating TRIM11 is upregulated in response to heatshock in cortical and hippocampal neurons. FIG. 42A depictsimmunoblotting of mouse primary cortical neurons treated with heat shockfor 30 minutes at 42° C. and recovered for 3 hours.

FIG. 42B depicts immunoblotting of mouse primary hippocampal neuronstreated with heat shock for 30 min at 42 C.° and recovered for 3 hours.FIG. 42C depicts semi-quantitative PCR analysis of TRIM11, HSP70, HSP90and GAPDH in response to heat shock in hippocampal neurons.

DETAILED DESCRIPTION

The present invention is related to the discovery of the role of membersof the tripartite motif (TRIM) family of proteins and the SUMO-dependentubiquitin ligase RNF4 in the recognition and degradation of misfoldedproteins, which play a role in the pathology of a variety ofneurodegenerative disorders.

In one aspect, the present invention provides compositions and methodsto treat or prevent a disease or disorder associated with misfoldedprotein or protein aggregates. It is demonstrated herein that TRIMproteins have roles in targeting misfolded proteins for proteosomaldegradation, as chaperone protein, and in disaggregating proteinaggregates or inclusions. Thus, in certain aspects, the presentinvention can be used to eliminate intracellular or extracellularmisfolded proteins, protein aggregates, or protein inclusions.

For example, in certain embodiments, the invention provides compositionsand methods to treat or prevent a neurodegenerative disorder in asubject in need thereof. For example, in certain embodiments, theinvention provides compositions and methods for the treatment orprevention of neurodegenerative disorders that are poly-glutamine(polyQ) disorders, where repeats of the CAG codon encode proteins withpolyglutamine tracts that can result in misfolded protein aggregates.Exemplary polyQ disorders include, but are not limited toSpinocerebellar ataxia (SCA) Type 1 (SCA1), SCA2, SCA3, SCA6, SCA7,SCA17, Huntington's disease, and Dentatorubral-pallidoluysian atrophy(DRPLA). In certain embodiments, the invention provides compositions andmethods for the treatment of neurodegenerative disorders associated withmisfolded proteins or protein aggregates, including, but not limited to,Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis(ALS), transmissible spongiform encephalopathies (prion disease),tauopathies, and Frontotemporal lobar degeneration (FTLD). However, thepresent invention is not limited to the treatment or prevention ofneurodegenerative disorders. Rather, the invention encompasses thetreatment or prevention of any disease or disorder associated with amisfolded protein or protein aggregate. Other such diseases anddisorders include, but is not limited to AL amyloidosis, AA amyloidosis,Familial Mediterranean fever, senile systemic amyloidosis, familialamyloidotic polyneuropathy, hemodialysis-related amyloidosis, ApoAIamyloidosis, ApoAII amyloidosis, ApoAIV amyloidosis, Finnish hereditaryamyloidosis, lysozyme amyloidosis, fibrinogen amyloidosis, Icelandichereditary cerebral amyloid angiopathy, type II diabetes, medullarycarcinoma of the thyroid, atrial amyloidosis, hereditary cerebralhemorrhage with amyloidosis, pituitary prolactinoma, injection-localizedamyloidosis, aortic medial amyloidosis, hereditary lattice cornealdystrophy, corneal amyloidosis associated with trichiasis, cataract,calcifying epithelial odontogenic tumor, pulmonary alveolar proteinosis,inclusion-body myostis, and cuteaneous lichen amyloidosis. In certainembodiments, the invention encompasses the treatment or prevention ofcancer associated with p53 mutant aggregates, including but not limitedto bladder carcinoma, astrocytoma, pharynx carcinoma, lymphoma, andadenocarcinoma.

In one aspect, the invention encompasses the use of one or more TRIMproteins to stabilize a misfolded protein. In certain aspects,stabilization of a functional misfolded protein via one or more TRIMproteins described herein can treat or prevent a disease or disorderassociated with the misfolded protein. For example, in one embodiment,stabilization of mutant cystic fibrosis transmembrane conductanceregulator (CFTR), via one or more TRIM proteins described herein, wouldallow mutant CFTR to function instead of being degraded. It isenvisioned that using TRIM proteins to stabilize misfolded proteins canbe used to treat cystic fibrosis and other diseases associated withdegradation of partially functional proteins. Stabilization of proteins,via one or more TRIM proteins described herein, can be used to treat anydisease or disorder associated with degradation of functional mutantprotein, including but not limited to cystic fibrosis and lysosomalstorage diseases such as Gaucher's disease and Fabry's disease.

In one aspect, the present invention provides compositions and methodsto increase the expression, activity, or both of a TRIM protein. Incertain embodiments, the composition comprises a nucleic acid molecule,expression vector, protein, peptide, small molecule, or the like, whichincreases the expression, activity, or both of one or more TRIMproteins.

In one aspect, the present invention provides compositions and methodsto increase the expression, activity, or both of one or moreSUMO-targeted ubiquitin ligases (STUbL). In certain embodiments, thecomposition comprises a nucleic acid molecule, expression vector,protein, peptide, small molecule, or the like, which increases theexpression, activity, or both of one or more STUbLs.

Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, the preferred methodsand materials are described.

As used herein, each of the following terms has the meaning associatedwith it in this section.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e., to at least one) of the grammatical object of thearticle. By way of example, “an element” means one element or more thanone element.

“About” as used herein when referring to a measurable value such as anamount, a temporal duration, and the like, is meant to encompassvariations of 20%, +10%, +5%, ±1%, or ±0.1% from the specified value, assuch variations are appropriate to perform the disclosed methods.

The term “abnormal” when used in the context of organisms, tissues,cells or components thereof, refers to those organisms, tissues, cellsor components thereof that differ in at least one observable ordetectable characteristic (e.g., age, treatment, time of day, etc.) fromthose organisms, tissues, cells or components thereof that display the“normal” (expected) respective characteristic. Characteristics which arenormal or expected for one cell or tissue type, might be abnormal for adifferent cell or tissue type.

A “disease” is a state of health of an animal wherein the animal cannotmaintain homeostasis, and wherein if the disease is not ameliorated thenthe animal's health continues to deteriorate.

In contrast, a “disorder” in an animal is a state of health in which theanimal is able to maintain homeostasis, but in which the animal's stateof health is less favorable than it would be in the absence of thedisorder. Left untreated, a disorder does not necessarily cause afurther decrease in the animal's state of health.

A disease or disorder is “alleviated” if the severity of a sign orsymptom of the disease or disorder, the frequency with which such a signor symptom is experienced by a patient, or both, is reduced.

An “effective amount” or “therapeutically effective amount” of acompound is that amount of a compound which is sufficient to provide abeneficial effect to the subject to which the compound is administered.An “effective amount” of a delivery vehicle is that amount sufficient toeffectively bind or deliver a compound.

As used herein, an “instructional material” includes a publication, arecording, a diagram, or any other medium of expression which can beused to communicate the usefulness of a compound, composition, vector,or delivery system of the invention in the kit for effecting alleviationof the various diseases or disorders recited herein. Optionally, oralternately, the instructional material can describe one or more methodsof alleviating the diseases or disorders in a cell or a tissue of amammal. The instructional material of the kit of the invention can, forexample, be affixed to a container which contains the identifiedcompound, composition, vector, or delivery system of the invention or beshipped together with a container which contains the identifiedcompound, composition, vector, or delivery system. Alternatively, theinstructional material can be shipped separately from the container withthe intention that the instructional material and the compound be usedcooperatively by the recipient.

The terms “patient,” “subject,” “individual,” and the like are usedinterchangeably herein, and refer to any animal, or cells thereofwhether in vitro or in vivo, amenable to the methods described herein.In certain non-limiting embodiments, the patient, subject or individualis a human.

A “therapeutic” treatment is a treatment administered to a subject whoexhibits signs or symptoms of a disease or disorder, for the purpose ofdiminishing or eliminating those signs or symptoms.

As used herein, “treating a disease or disorder” means reducing theseverity and/or frequency with which a sign or symptom of the disease ordisorder is experienced by a patient.

The phrase “biological sample” as used herein, is intended to includeany sample comprising a cell, a tissue, or a bodily fluid in whichexpression of a nucleic acid or polypeptide is present or can bedetected. Samples that are liquid in nature are referred to herein as“bodily fluids.” Biological samples may be obtained from a patient by avariety of techniques including, for example, by scraping or swabbing anarea of the subject or by using a needle to obtain bodily fluids.Methods for collecting various body samples are well known in the art.

As used herein, an “immunoassay” refers to any binding assay that usesan antibody capable of binding specifically to a target molecule todetect and quantify the target molecule.

By the term “specifically binds,” as used herein with respect to anantibody, is meant an antibody which recognizes a specific antigen, butdoes not substantially recognize or bind other molecules in a sample.For example, an antibody that specifically binds to an antigen from onespecies may also bind to that antigen from one or more species. But,such cross-species reactivity does not itself alter the classificationof an antibody as specific. In another example, an antibody thatspecifically binds to an antigen may also bind to different allelicforms of the antigen. However, such cross reactivity does not itselfalter the classification of an antibody as specific.

In some instances, the terms “specific binding” or “specificallybinding,” can be used in reference to the interaction of an antibody, aprotein, or a peptide with a second chemical species, to mean that theinteraction is dependent upon the presence of a particular structure(e.g., an antigenic determinant or epitope) on the chemical species; forexample, an antibody recognizes and binds to a specific proteinstructure rather than to proteins generally. If an antibody is specificfor epitope “A”, the presence of a molecule containing epitope A (orfree, unlabeled A), in a reaction containing labeled “A” and theantibody, will reduce the amount of labeled A bound to the antibody.

A “coding region” of a gene consists of the nucleotide residues of thecoding strand of the gene and the nucleotides of the non-coding strandof the gene which are homologous with or complementary to, respectively,the coding region of an mRNA molecule which is produced by transcriptionof the gene.

A “coding region” of a mRNA molecule consists of the nucleotide residuesof the mRNA molecule which are matched with an anti-codon region of atransfer RNA molecule during translation of the mRNA molecule or whichencode a stop codon. The coding region may thus include nucleotideresidues comprising codons for amino acid residues which are not presentin the mature protein encoded by the mRNA molecule (e.g., amino acidresidues in a protein export signal sequence).

“Complementary” as used herein to refer to a nucleic acid, refers to thebroad concept of sequence complementarity between regions of two nucleicacid strands or between two regions of the same nucleic acid strand. Itis known that an adenine residue of a first nucleic acid region iscapable of forming specific hydrogen bonds (“base pairing”) with aresidue of a second nucleic acid region which is antiparallel to thefirst region if the residue is thymine or uracil. Similarly, it is knownthat a cytosine residue of a first nucleic acid strand is capable ofbase pairing with a residue of a second nucleic acid strand which isantiparallel to the first strand if the residue is guanine. A firstregion of a nucleic acid is complementary to a second region of the sameor a different nucleic acid if, when the two regions are arranged in anantiparallel fashion, at least one nucleotide residue of the firstregion is capable of base pairing with a residue of the second region.Preferably, the first region comprises a first portion and the secondregion comprises a second portion, whereby, when the first and secondportions are arranged in an antiparallel fashion, at least about 50%,and preferably at least about 75%, at least about 90%, or at least about95% of the nucleotide residues of the first portion are capable of basepairing with nucleotide residues in the second portion. More preferably,all nucleotide residues of the first portion are capable of base pairingwith nucleotide residues in the second portion.

“Isolated” means altered or removed from the natural state. For example,a nucleic acid or a peptide naturally present in its normal context in aliving animal is not “isolated,” but the same nucleic acid or peptidepartially or completely separated from the coexisting materials of itsnatural context is “isolated.” An isolated nucleic acid or protein canexist in substantially purified form, or can exist in a non-nativeenvironment such as, for example, a host cell.

An “isolated nucleic acid” refers to a nucleic acid segment or fragmentwhich has been separated from sequences which flank it in a naturallyoccurring state, i.e., a DNA fragment which has been removed from thesequences which are normally adjacent to the fragment, i.e., thesequences adjacent to the fragment in a genome in which it naturallyoccurs. The term also applies to nucleic acids which have beensubstantially purified from other components which naturally accompanythe nucleic acid, i.e., RNA or DNA or proteins, which naturallyaccompany it in the cell. The term therefore includes, for example, arecombinant DNA which is incorporated into a vector, into anautonomously replicating plasmid or virus, or into the genomic DNA of aprokaryote or eukaryote, or which exists as a separate molecule (i.e.,as a cDNA or a genomic or cDNA fragment produced by PCR or restrictionenzyme digestion) independent of other sequences. It also includes arecombinant DNA which is part of a hybrid gene encoding additionalpolypeptide sequence.

In the context of the present invention, the following abbreviations forthe commonly occurring nucleic acid bases are used. “A” refers toadenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refersto thymidine, and “U” refers to uridine.

The term “polynucleotide” as used herein is defined as a chain ofnucleotides. Furthermore, nucleic acids are polymers of nucleotides.Thus, nucleic acids and polynucleotides as used herein areinterchangeable. One skilled in the art has the general knowledge thatnucleic acids are polynucleotides, which can be hydrolyzed into themonomeric “nucleotides.” The monomeric nucleotides can be hydrolyzedinto nucleosides. As used herein polynucleotides include, but are notlimited to, all nucleic acid sequences which are obtained by any meansavailable in the art, including, without limitation, recombinant means,i.e., the cloning of nucleic acid sequences from a recombinant libraryor a cell genome, using ordinary cloning technology and PCR, and thelike, and by synthetic means.

As used herein, the terms “peptide,” “polypeptide,” and “protein” areused interchangeably, and refer to a compound comprised of amino acidresidues covalently linked by peptide bonds. A protein or peptide mustcontain at least two amino acids, and no limitation is placed on themaximum number of amino acids that can comprise a protein's or peptide'ssequence. Polypeptides include any peptide or protein comprising two ormore amino acids joined to each other by peptide bonds. As used herein,the term refers to both short chains, which also commonly are referredto in the art as peptides, oligopeptides and oligomers, for example, andto longer chains, which generally are referred to in the art asproteins, of which there are many types. “Polypeptides” include, forexample, biologically active fragments, substantially homologouspolypeptides, oligopeptides, homodimers, heterodimers, variants ofpolypeptides, modified polypeptides, derivatives, analogs, fusionproteins, among others. The polypeptides include natural peptides,recombinant peptides, synthetic peptides, or a combination thereof.

As used herein, “conjugated” refers to covalent attachment of onemolecule to a second molecule.

“Variant” as the term is used herein, is a nucleic acid sequence or apeptide sequence that differs in sequence from a reference nucleic acidsequence or peptide sequence respectively, but retains essentialbiological properties of the reference molecule. Changes in the sequenceof a nucleic acid variant may not alter the amino acid sequence of apeptide encoded by the reference nucleic acid, or may result in aminoacid substitutions, additions, deletions, fusions and truncations.Changes in the sequence of peptide variants are typically limited orconservative, so that the sequences of the reference peptide and thevariant are closely similar overall and, in many regions, identical. Avariant and reference peptide can differ in amino acid sequence by oneor more substitutions, additions, deletions in any combination. Avariant of a nucleic acid or peptide can be a naturally occurring suchas an allelic variant, or can be a variant that is not known to occurnaturally. Non-naturally occurring variants of nucleic acids andpeptides may be made by mutagenesis techniques or by direct synthesis.

As used herein, a “modulator of one or more TRIM proteins” is a compoundthat modifies the expression, activity or biological function of theTRIM protein as compared to the expression, activity or biologicalfunction of the TRIM protein in the absence of the modulator.

As used herein, a “modulator of RNF4” is a compound that modifies theexpression, activity or biological function of RNF4 as compared to theexpression, activity or biological function of RNF4 in the absence ofthe modulator.

Ranges: throughout this disclosure, various aspects of the invention canbe presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. Thisapplies regardless of the breadth of the range.

DESCRIPTION

In one aspect, the present invention provides compositions and methodsto treat or prevent a disease or disorder associated with misfoldedproteins or protein aggregates. For example, the present inventionprovides compositions and methods to increase the recognition andelimination of misfolded proteins. In certain embodiments, the inventionprovides for the SUMO-mediated ubiquitination and eventual degradationof misfolded protein. In certain embodiments, the invention provides forthe disaggregation of protein aggregates or inclusions. The presentinvention can thus be used to eliminate misfolded proteins, proteinaggregates, or protein inclusions, both intracellularly orextracellularly.

The present invention is related to the discovery of the role of membersof the tripartite motif (TRIM) family of proteins and the SUMO-targetedubiquitin ligase (STUbL), RNF4, in the recognition and degradation ofmisfolded proteins, which play a role in the pathology of a variety ofdiseases and disorders, including many neurodegenerative diseases anddisorders.

The data presented herein demonstrates that members of the TRIM proteinfamily co-localize with misfolded proteins and mediate the degradationof misfolded proteins. Further, it is described herein that RNF4 is anubiquitin ligase which mediates the ubiquitination and degradation ofmisfolded proteins. Thus, the present invention provides compositionsthat increase the expression, activity, or both of one or more TRIMproteins, one or more STUbLs, or a combination thereof. For example, itis demonstrated that nucleic acid molecules encoding a TRIM protein andrecombinant TRIM proteins promotes the degradation of misfolded protein.

In one embodiment, the composition comprises a modulator of theexpression or activity of one or more TRIM proteins. For example, in oneembodiment, the modulator increases the expression or activity of one ormore TRIM proteins. The one or more TRIM proteins, include, any memberof the TRIM protein family, including mammalian and non-mammalianmembers. In certain embodiments, the modulator increases the expressionor activity of one or more of human TRIM3, TRIM4, TRIM5, TRIM6, TRIM7,TRIM9, TRIM11, TRIM13, TRIM14, TRIM15, TRIM16, TRIM17, TRIM19 (alsoreferred to herein as “PML”), TRIM20, TRIM21, TRIM24, TRIM25, TRIM27,TRIM28, TRIM29, TRIM32, TRIM34, TRIM39, TRIM43, TRIM44, TRIM45, TRIM46,TRIM49, TRIM50, TRIM52, TRIM58, TRIM59, TRIM65, TRIM67, TRIM69, TRIM70,TRIM74 and TRIM75; and mouse TRIM30.

In one embodiment, the composition comprises a modulator of one or moreSTUbLs. For example, in one embodiment, the modulator increases theexpression or activity of one or more STUbLs. Exemplary STUbLs include,but are not limited to RNF4 and RNF111 (also known as Arkadia).

In one embodiment, the composition comprises a modulator of one or moreTRIM proteins and a modulator of one or more STUbLs.

The present invention provides a method for treating or preventing adisease or disorder associated with misfolded proteins or proteinaggregates, in a subject in need. It is found herein that increasing thelevel of expression or activity of a TRIM protein or STUbL, can promotethe degradation of misfolded protein, thereby treating the disease ordisorder in the subject.

Examples of neurodegenerative diseases or disorders which may be treatedor prevented by the compositions and methods of this invention include,but are not limited to polyQ disorders such as SCA1, SCA2, SCA3, SCA6,SCA7, SCA17, Huntington's disease, Dentatorubral-pallidoluysian atrophy(DRPLA), Alzheimer's disease, Parkinson's disease, amyotrophic lateralsclerosis (ALS), transmissible spongiform encephalopathies (priondisease), tauopathies, and Frontotemporal lobar degeneration (FTLD).However, the present invention is not limited to the treatment orprevention of neurodegenerative disorders. Rather, the inventionencompasses the treatment or prevention of any disease or disorderassociated with a misfolded protein or protein aggregate. Other suchdiseases and disorders include, but is not limited to AL amyloidosis, AAamyloidosis, Familial Mediterranean fever, senile systemic amyloidosis,familial amyloidotic polyneuropathy, hemodialysis-related amyloidosis,ApoAI amyloidosis, ApoAII amyloidosis, ApoAIV amyloidosis, Finnishhereditary amyloidosis, lysozyme amyloidosis, fibrinogen amyloidosis,Icelandic hereditary cerebral amyloid angiopathy, type II diabetes,medullary carcinoma of the thyroid, atrial amyloidosis, hereditarycerebral hemorrhage with amyloidosis, pituitary prolactinoma,injection-localized amyloidosis, aortic medial amyloidosis, hereditarylattice corneal dystrophy, corneal amyloidosis associated withtrichiasis, cataract, calcifying epithelial odontogenic tumor, pulmonaryalveolar proteinosis, inclusion-body myostis, and cuteaneous lichenamyloidosis. In certain embodiments, the invention encompasses thetreatment or prevention of cancer associated with p53 mutant aggregates,including but not limited to bladder carcinoma, astrocytoma, pharynxcarcinoma, lymphoma, and adenocarcinoma.

In one aspect, the invention encompasses the use of one or more TRIMproteins to stabilize a misfolded protein. In certain aspects,stabilization of a functional misfolded protein via one or more TRIMproteins described herein can treat or prevent a disease or disorderassociated with the misfolded protein, including but not limited tocystic fibrosis and lysosomal storage diseases such as Gaucher's diseaseand Fabry's disease.

In one aspect, the present invention provides a method to diagnose adisease or disorder associated with a misfolded protein or proteinaggregate. For example, in one embodiment, one or more TRIM proteins orone or more STUbLs are used as diagnostic markers.

In one aspect, the present invention is directed to compositions andmethods for manufacture of a recombinant protein of interest. Forexample, in certain embodiments, the one or more TRIM proteins and oneor more STUbLs can be used to disaggregate protein aggregates ofrecombinant protein of interest.

Compositions

In various embodiments, the present invention includes modulatorcompositions and methods of preventing and treating a disease ordisorder associated with misfolded protein or protein aggregates. Invarious embodiments, the modulator compositions and methods ofpreventing or treating of the invention modulate the level or activityof a gene, or gene product. In some embodiments, the modulatorcomposition of the invention is an activator that increases the level oractivity of a gene, or gene product.

It will be understood by one skilled in the art, based upon thedisclosure provided herein, that modulating a gene, or gene product,encompasses modulating the level or activity of a gene, or gene product,including, but not limited to, modulating the transcription,translation, splicing, degradation, enzymatic activity, bindingactivity, or combinations thereof. Thus, modulating the level oractivity of a gene, or gene product, includes, but is not limited to,modulating transcription, translation, degradation, splicing, orcombinations thereof, of a nucleic acid; and it also includes modulatingany activity of polypeptide gene product as well.

In one embodiment, the modulator increases the expression or activity ofa gene or gene product by increasing production of the gene or geneproduct, for example by modulating transcription of the gene ortranslation of the gene product. In one embodiment, the modulatorincreases the expression or activity of a gene or gene product byproviding exogenous gene or gene product. For example, in certainembodiments, the modulator comprises an isolated nucleic acid encodingone or more TRIM proteins or one or more STUbLs. In one embodiment, themodulator comprises an isolated nucleic acid encoding one or more TRIMproteins and one or more STUbLs. In certain embodiments, the modulatorcomprises an isolated peptide comprising one or more TRIM proteins orone or more STUbLs. In one embodiment, the modulator comprises anisolated peptide comprising one or more TRIM proteins and one or moreSTUbLs. In one embodiment, the modulator increases the expression oractivity of a gene or gene product by inhibiting the degradation of thegene or gene product. For example, in one embodiment, the modulatordecreases the ubiquitination, proteosomal degradation, or proteolysis ofone or more TRIM proteins or one or more STUbLs. In one embodiment, themodulator increases the stability or half-life of a gene product.

In various embodiments, the modulated gene, or gene product, is one ormore TRIM proteins. For example, it is described herein that TRIMproteins recognize misfolded proteins and mediate the degradation ofmisfolded proteins and protein aggregates. In one embodiment, the geneor gene product is one or more STUbLs. For example, it is describedherein that RNF4, a member of the STUbl family of proteins, mediates thedegradation of misfolded proteins and protein aggregates.

Modulation of a gene, or gene product, can be assessed using a widevariety of methods, including those disclosed herein, as well as methodsknown in the art or to be developed in the future. That is, theroutineer would appreciate, based upon the disclosure provided herein,that modulating the level or activity of a gene, or gene product, can bereadily assessed using methods that assess the level of a nucleic acidencoding a gene product (e.g., mRNA), the level of polypeptide geneproduct present in a biological sample, the activity of polypeptide geneproduct present in a biological sample, or combinations thereof.

The modulator compositions and methods of the invention that modulatethe level or activity of a gene, or gene product, include, but shouldnot be construed as being limited to, a chemical compound, a protein, apeptide, a peptidomemetic, an antibody, a ribozyme, a small moleculechemical compound, a nucleic acid, a vector, an antisense nucleic acidmolecule (e.g., siRNA, miRNA, etc.), or combinations thereof. One ofskill in the art would readily appreciate, based on the disclosureprovided herein, that a modulator composition encompasses a chemicalcompound that modulates the level or activity of a gene, or geneproduct. Additionally, a modulator composition encompasses a chemicallymodified compound, and derivatives, as is well known to one of skill inthe chemical arts.

In one embodiment, the modulator composition of the present invention isan agonist, which increases the expression, activity, or biologicalfunction of a gene or gene product. For example, in certain embodiments,the modulator of the present invention is an agonist of one or more TRIMproteins or one or more STUbLs.

Further, one of skill in the art would, when equipped with thisdisclosure and the methods exemplified herein, appreciate thatmodulators include such modulators as discovered in the future, as canbe identified by well-known criteria in the art of pharmacology, such asthe physiological results of modulation of the genes, and gene products,as described in detail herein and/or as known in the art. Therefore, thepresent invention is not limited in any way to any particular modulatorcomposition as exemplified or disclosed herein; rather, the inventionencompasses those modulator compositions that would be understood by theroutineer to be useful as are known in the art and as are discovered inthe future.

Further methods of identifying and producing modulator compositions arewell known to those of ordinary skill in the art. Alternatively, amodulator can be synthesized chemically. Further, the routineer wouldappreciate, based upon the teachings provided herein, that a modulatorcomposition can be obtained from a recombinant organism. Compositionsand methods for chemically synthesizing modulators and for obtainingthem from natural sources are well known in the art and are described inthe art.

One of skill in the art will appreciate that a modulator can beadministered as a small molecule chemical, a polypeptide, a peptide, anantibody, a nucleic acid construct encoding a protein, an antisensenucleic acid, a nucleic acid construct encoding an antisense nucleicacid, or combinations thereof. Numerous vectors and other compositionsand methods are well known for administering a protein or a nucleic acidconstruct encoding a protein to cells or tissues. Therefore, theinvention includes a peptide or a nucleic acid encoding a peptide thatis modulator of a gene, or gene product. For example, the inventionincludes a peptide or a nucleic acid encoding a peptide that comprisesone or more TRIM proteins, one or more STUbLs, or a combination thereof.(Sambrook et al., 2001, Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Laboratory, New York; Ausubel et al., 1997, CurrentProtocols in Molecular Biology, John Wiley & Sons, New York).

Peptides

In one embodiment, the composition of the present invention comprisesone or more peptides. For example, in one embodiment, a peptide of thecomposition comprises an amino acid sequence of one or more TRIMproteins. For example, in one embodiment, the peptide comprises one ormore of TRIM5δ, TRIM 11, TRIM419, TRIM 21, TRIM27, and TRIM32. Incertain embodiments, the peptide comprises an amino acid sequence of oneor more STUbLs. For example, in one embodiment, the peptide comprisesone or more of RNF4 and RNF111 (Arkadia).

Exemplary amino acid sequences of TRIM proteins, and cDNA nucleotidesequences encoding TRIM proteins is provided in Table 1 below.

TABLE 1 TRIM protein nucleotide and amino acid sequences NucleotideProtein Accession Nucleotide Accession Amino Acid Name Number SequenceNumber Sequence TRIM1 NM_012216.3 SEQ ID NO: 1 NP_036348.2 SEQ ID NO: 2TRIM2 NM_015271.4 SEQ ID NO: 3 NP_056086.2 SEQ ID NO: 4 TRIM3NM_006458.3 SEQ ID NO: 5 NP_006449.2 SEQ ID NO: 6 TRIM4 NM_033017.3 SEQID NO: 7 NP_148977.2 SEQ ID NO: 8 TRIM5 NM_033034.2 SEQ ID NO: 9NP_149023.2 SEQ ID NO: 10 TRIM6 NM_001003818.2 SEQ ID NO: 11NP_001003818.1 SEQ ID NO: 12 TRIM7 NM_033342.3 SEQ ID NO: 13 NP_203128.1SEQ ID NO: 14 TRIM8 NM_030912.2 SEQ ID NO: 15 NP_112174.2 SEQ ID NO: 16TRIM9 NM_015163.5 SEQ ID NO: 17 NP_055978.4 SEQ ID NO: 18 TRIM10NM_006778.3 SEQ ID NO: 19 NP_006769.2 SEQ ID NO: 20 TRIM11 NM_145214.2SEQ ID NO: 21 NP_660215.1 SEQ ID NO: 22 TRIM12 NM_023835.2 SEQ ID NO: 23NP_076324.2 SEQ ID NO: 24 TRIM13 NM_005798.4 SEQ ID NO: 25 NP_005789.2SEQ ID NO: 26 TRIM14 NM_014788.3 SEQ ID NO: 27 NP_055603.2 SEQ ID NO: 28TRIM15 NM_033229.2 SEQ ID NO: 29 NP_150232.2 SEQ ID NO: 30 TRIM16NM_006470.3 SEQ ID NO: 31 NP_006461.3 SEQ ID NO: 32 TRIM17 NM_016102.3SEQ ID NO: 33 NP_057186.1 SEQ ID NO: 34 TRIM18 NM_000381.3 SEQ ID NO: 35NP_000372.1 SEQ ID NO: 36 TRIM19 NM_033238.2 SEQ ID NO: 37 NP_150241.2SEQ ID NO: 38 TRIM20 NM_000243.2 SEQ ID NO: 39 NP_000234.1 SEQ ID NO: 40TRIM21 NM_003141.3 SEQ ID NO: 41 NP_003132.2 SEQ ID NO: 42 TRIM22NM_006074.4 SEQ ID NO: 43 NP_006065.2 SEQ ID NO: 44 TRIM23 NM_001656.3SEQ ID NO: 45 NP_001647.1 SEQ ID NO: 46 TRIM24 NM_015905.2 SEQ ID NO: 47NP_056989.2 SEQ ID NO: 48 TRIM25 NM_005082.4 SEQ ID NO: 49 NP_005073.2SEQ ID NO: 50 TRIM26 NM_003449.4 SEQ ID NO: 51 NP_003440.1 SEQ ID NO: 52TRIM27 NM_006510.4 SEQ ID NO: 53 NP_006501.1 SEQ ID NO: 54 TRIM28NM_005762.2 SEQ ID NO: 55 NP_005753.1 SEQ ID NO: 56 TRIM29 NM_012101.3SEQ ID NO: 57 NP_036233.2 SEQ ID NO: 58 TRIM30 NM_009099.2 SEQ ID NO: 59NP_033125.2 SEQ ID NO: 60 TRIM31 NM_007028.4 SEQ ID NO: 61 NP_008959.3SEQ ID NO: 62 TRIM32 NM_012210.3 SEQ ID NO: 63 NP_036342.2 SEQ ID NO: 64TRIM33 NM_015906.3 SEQ ID NO: 65 NP_056990.3 SEQ ID NO: 66 TRIM34NM_021616.5 SEQ ID NO: 67 NP_067629.2 SEQ ID NO: 68 TRIM35 NM_171982.4SEQ ID NO: 69 NP_741983.2 SEQ ID NO: 70 TRIM36 NM_018700.3 SEQ ID NO: 71NP_061170.2 SEQ ID NO: 72 TRIM37 NM_015294.4 SEQ ID NO: 73 NP_056109.1SEQ ID NO: 74 TRIM38 NM_006355.4 SEQ ID NO: 75 NP_006346.1 SEQ ID NO: 76TRIM39 NM_021253.3 SEQ ID NO: 77 NP_067076.2 SEQ ID NO: 78 TRIM40NM_001286633.1 SEQ ID NO: 79 NP_001273562.1 SEQ ID NO: 80 TRIM41NM_033549.4 SEQ ID NO: 81 NP_291027.3 SEQ ID NO: 82 TRIM42 NM_152616.4SEQ ID NO: 83 NP_689829.3 SEQ ID NO: 84 TRIM43 NM_138800.1 SEQ ID NO: 85NP_620155.1 SEQ ID NO: 86 TRIM44 NM_017583.5 SEQ ID NO: 87 NP_060053.2SEQ ID NO: 88 TRIM45 NM_025188.3 SEQ ID NO: 89 NP_079464.2 SEQ ID NO: 90TRIM46 NM_025058.4 SEQ ID NO: 91 NP_079334.3 SEQ ID NO: 92 TRIM47NM_033452.2 SEQ ID NO: 93 NP_258411.2 SEQ ID NO: 94 TRIM48 NM_024114.3SEQ ID NO: 95 NP_077019.2 SEQ ID NO: 96 TRIM49 NM_020358.2 SEQ ID NO: 97NP_065091.1 SEQ ID NO: 98 TRIM50 NM_178125.3 SEQ ID NO: 99 NP_835226.2SEQ ID NO: 100 TRIM51 NM_032681.3 SEQ ID NO: 101 NP_116070.2 SEQ ID NO:102 TRIM52 NM_032765.2 SEQ ID NO: 103 NP_116154.1 SEQ ID NO: 104 TRIM54NM_032546.3 SEQ ID NO: 105 NP_115935.3 SEQ ID NO: 106 TRIM55 NM_184085.1SEQ ID NO: 107 NP_908973.1 SEQ ID NO: 108 TRIM56 NM_030961.2 SEQ ID NO:109 NP_112223.1 SEQ ID NO: 110 TRIM58 NM_015431.3 SEQ ID NO: 111NP_056246.3 SEQ ID NO: 112 TRIM59 NM_173084.2 SEQ ID NO: 113 NP_775107.1SEQ ID NO: 114 TRIM60 NM_152620.2 SEQ ID NO: 115 NP_689833.1 SEQ ID NO:116 TRIM61 NM_001012414.2 SEQ ID NO: 117 NP_001012414.1 SEQ ID NO: 118TRIM62 NM_018207.2 SEQ ID NO: 119 NP_060677.2 SEQ ID NO: 120 TRIM63NM_032588.3 SEQ ID NO: 121 NP_115977.2 SEQ ID NO: 122 TRIM64NM_001136486.1 SEQ ID NO: 123 NP_001129958.1 SEQ ID NO: 124 TRIM65NM_173547.3 SEQ ID NO: 125 NP_775818.2 SEQ ID NO: 126 TRIM66 NM_014818.1SEQ ID NO: 127 NP_055633.1 SEQ ID NO: 128 TRIM67 NM_001004342.3 SEQ IDNO: 129 NP_001004342.3 SEQ ID NO: 130 TRIM68 NM_018073.7 SEQ ID NO: 131NP_060543.5 SEQ ID NO: 132 TRIM69 NM_080745.4 SEQ ID NO: 133 NP_542783.2SEQ ID NO: 134 TRIM70 NM_001037330.1 SEQ ID NO: 135 NP_001032407.1 SEQID NO: 136 TRIM71 NM_001039111.2 SEQ ID NO: 137 NP_001034200.1 SEQ IDNO: 138 TRIM72 NM_001008274.3 SEQ ID NO: 139 NP_001008275.2 SEQ ID NO:140 TRIM73 NM_198924.3 SEQ ID NO: 141 NP_944606.2 SEQ ID NO: 142 TRIM74NM_198853.2 SEQ ID NO: 143 NP_942150.1 SEQ ID NO: 144 TRIM75NM_001033429.2 SEQ ID NO: 145 NP_001028601.1 SEQ ID NO: 146 TRIM76NM_153610.4 SEQ ID NO: 164 NP_705838.3 SEQ ID NO: 165 TRIM77NM_001146162.1 SEQ ID NO: 166 NP_001139634.1 SEQ ID NO: 167

The invention should also be construed to include any form of a peptidehaving substantial homology to the peptides disclosed herein.Preferably, a peptide which is “substantially homologous” is about 50%homologous, more preferably about 70% homologous, even more preferablyabout 80% homologous, more preferably about 90% homologous, even morepreferably, about 95% homologous, and even more preferably about 99%homologous to amino acid sequence of the peptides disclosed herein.

In one embodiment, the composition of the invention comprises a peptide,a fragment of a peptide, a homolog, a variant, a derivative or a salt ofa peptide described herein. For example, in certain embodiments, thecomposition comprises a peptide comprising one or more TRIM proteins, afragment of one or more TRIM proteins, a homolog of one or more TRIMproteins, a variant of one or more TRIM proteins, a derivative of one ormore TRIM proteins, or a salt of one or more TRIM proteins. In certainembodiments, the composition comprises a peptide comprising one or moreSTUbLs, a fragment of one or more STUbLs, a homolog of one or moreSTUbLs, a variant of one or more STUbLs, a derivative of one or moreSTUbLs, or a salt of one or more STUbLs.

In one embodiment, the composition comprises a combination of thepeptides described herein. For example, in certain embodiments, thecomposition comprises a peptide comprising one or more TRIM proteins anda peptide comprising one or more STUbLs. In one embodiment, thecomposition comprises a peptide comprising one or more TRIM proteins andone or more STUbLs.

In certain embodiments, the peptide comprises a targeting domain, whichtargets the peptide to a desired location. For example, in certainembodiments, the targeting domain binds to a targeted cell, protein, orprotein aggregate, thereby delivering the therapeutic peptide to adesired location. For example, in one embodiment, the targeting domainis directed to bind to a protein or protein aggregate associated with adisease or disorder, including but not limited to the proteins andprotein aggregates of amyloid-beta, alpha-synuclein, tau, prions, SOD1,TDP-43, FUS, p53 mutants, and proteins associated with polyglutaminerepeats, such as huntingtin, ataxins.

In certain embodiments, the targeting domain comprises a peptide,nucleic acid, small molecule, or the like, which has the ability to bindto the targeted cell, protein, or protein aggregate. For example, in oneembodiment, the targeting domain comprises an antibody or antibodyfragment which binds to a targeted cell, protein, or protein aggregate.

The peptide of the present invention may be made using chemical methods.For example, peptides can be synthesized by solid phase techniques(Roberge J Y et al (1995) Science 269: 202-204), cleaved from the resin,and purified by preparative high performance liquid chromatography.Automated synthesis may be achieved, for example, using the ABI 431 APeptide Synthesizer (Perkin Elmer) in accordance with the instructionsprovided by the manufacturer.

The peptide may alternatively be made by recombinant means or bycleavage from a longer polypeptide. The composition of a peptide may beconfirmed by amino acid analysis or sequencing.

The variants of the peptides according to the present invention may be(i) one in which one or more of the amino acid residues are substitutedwith a conserved or non-conserved amino acid residue (preferably aconserved amino acid residue) and such substituted amino acid residuemay or may not be one encoded by the genetic code, (ii) one in whichthere are one or more modified amino acid residues, e.g., residues thatare modified by the attachment of substituent groups, (iii) one in whichthe peptide is an alternative splice variant of the peptide of thepresent invention, (iv) fragments of the peptides and/or (v) one inwhich the peptide is fused with another peptide, such as a leader orsecretory sequence or a sequence which is employed for purification (forexample, His-tag) or for detection (for example, Sv5 epitope tag). Thefragments include peptides generated via proteolytic cleavage (includingmulti-site proteolysis) of an original sequence. Variants may bepost-translationally, or chemically modified. Such variants are deemedto be within the scope of those skilled in the art from the teachingherein.

The peptides of the invention can be post-translationally modified. Forexample, post-translational modifications that fall within the scope ofthe present invention include signal peptide cleavage, glycosylation,acetylation, isoprenylation, proteolysis, myristoylation, proteinfolding and proteolytic processing, etc. Some modifications orprocessing events require introduction of additional biologicalmachinery. For example, processing events, such as signal peptidecleavage and core glycosylation, are examined by adding caninemicrosomal membranes or Xenopus egg extracts (U.S. Pat. No. 6,103,489)to a standard translation reaction.

The peptides of the invention may include unnatural amino acids formedby post-translational modification or by introducing unnatural aminoacids during translation. A variety of approaches are available forintroducing unnatural amino acids during protein translation. By way ofexample, special tRNAs, such as tRNAs which have suppressor properties,suppressor tRNAs, have been used in the process of site-directednon-native amino acid replacement (SNAAR). In SNAAR, a unique codon isrequired on the mRNA and the suppressor tRNA, acting to target anon-native amino acid to a unique site during the protein synthesis(described in WO90/05785). However, the suppressor tRNA must not berecognizable by the aminoacyl tRNA synthetases present in the proteintranslation system. In certain cases, a non-native amino acid can beformed after the tRNA molecule is aminoacylated using chemical reactionswhich specifically modify the native amino acid and do not significantlyalter the functional activity of the aminoacylated tRNA. These reactionsare referred to as post-aminoacylation modifications. For example, theepsilon-amino group of the lysine linked to its cognate tRNA(tRNA_(LYS)), could be modified with an amine specific photoaffinitylabel.

The peptides of the invention may be conjugated with other molecules,such as proteins, to prepare fusion proteins. This may be accomplished,for example, by the synthesis of N-terminal or C-terminal fusionproteins provided that the resulting fusion protein retains thefunctionality of the peptide of the invention.

Cyclic derivatives of the peptides the invention are also part of thepresent invention. Cyclization may allow the peptide to assume a morefavorable conformation for association with other molecules. Cyclizationmay be achieved using techniques known in the art. For example,disulfide bonds may be formed between two appropriately spacedcomponents having free sulfhydryl groups, or an amide bond may be formedbetween an amino group of one component and a carboxyl group of anothercomponent. Cyclization may also be achieved using anazobenzene-containing amino acid as described by Ulysse, L., et al., J.Am. Chem. Soc. 1995, 117, 8466-8467. The components that form the bondsmay be side chains of amino acids, non-amino acid components or acombination of the two. In an embodiment of the invention, cyclicpeptides may comprise a beta-turn in the right position. Beta-turns maybe introduced into the peptides of the invention by adding the aminoacids Pro-Gly at the right position.

It may be desirable to produce a cyclic peptide which is more flexiblethan the cyclic peptides containing peptide bond linkages as describedabove. A more flexible peptide may be prepared by introducing cysteinesat the right and left position of the peptide and forming a disulphidebridge between the two cysteines. The two cysteines are arranged so asnot to deform the beta-sheet and turn. The peptide is more flexible as aresult of the length of the disulfide linkage and the smaller number ofhydrogen bonds in the beta-sheet portion. The relative flexibility of acyclic peptide can be determined by molecular dynamics simulations.

The peptides of the invention may be converted into pharmaceutical saltsby reacting with inorganic acids such as hydrochloric acid, sulfuricacid, hydrobromic acid, phosphoric acid, etc., or organic acids such asformic acid, acetic acid, propionic acid, glycolic acid, lactic acid,pyruvic acid, oxalic acid, succinic acid, malic acid, tartaric acid,citric acid, benzoic acid, salicylic acid, benezenesulfonic acid, andtoluenesulfonic acids.

Peptides of the invention may also have modifications. Modifications(which do not normally alter primary sequence) include in vivo, or invitro chemical derivatization of polypeptides, e.g., acetylation, orcarboxylation. Also included are modifications of glycosylation, e.g.,those made by modifying the glycosylation patterns of a polypeptideduring its synthesis and processing or in further processing steps;e.g., by exposing the polypeptide to enzymes which affect glycosylation,e.g., mammalian glycosylating or deglycosylating enzymes. Also embracedare sequences which have phosphorylated amino acid residues, e.g.,phosphotyrosine, phosphoserine, or phosphothreonine.

Also included are peptides which have been modified using ordinarymolecular biological techniques so as to improve their resistance toproteolytic degradation or to optimize solubility properties or torender them more suitable as a therapeutic agent. Such variants includethose containing residues other than naturally-occurring L-amino acids,e.g., D-amino acids or non-naturally-occurring synthetic amino acids.The peptides of the invention may further be conjugated to non-aminoacid moieties that are useful in their therapeutic application. Inparticular, moieties that improve the stability, biological half-life,water solubility, and/or immunologic characteristics of the peptide areuseful. A non-limiting example of such a moiety is polyethylene glycol(PEG).

Covalent attachment of biologically active compounds to water-solublepolymers is one method for alteration and control of biodistribution,pharmacokinetics, and often, toxicity for these compounds (Duncan etal., 1984, Adv. Polym. Sci. 57:53-101). Many water-soluble polymers havebeen used to achieve these effects, such as poly(sialic acid), dextran,poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA),poly(N-vinylpyrrolidone) (PVP), poly(vinyl alcohol) (PVA), poly(ethyleneglycol-co-propylene glycol), poly(N-acryloyl morpholine (PAcM), andpoly(ethylene glycol) (PEG) (Powell, 1980, Polyethylene glycol. In R. L.Davidson (Ed.) Handbook of Water Soluble Gums and Resins. McGraw-Hill,New York, chapter 18). PEG possess an ideal set of properties: very lowtoxicity (Pang, 1993, J. Am. Coll. Toxicol. 12: 429-456) excellentsolubility in aqueous solution (Powell, supra), low immunogenicity andantigenicity (Dreborg et al., 1990, Crit. Rev. Ther. Drug Carrier Syst.6: 315-365). PEG-conjugated or “PEGylated” protein therapeutics,containing single or multiple chains of polyethylene glycol on theprotein, have been described in the scientific literature (Clark et al.,1996, J. Biol. Chem. 271: 21969-21977; Hershfield, 1997, Biochemistryand immunology of poly(ethylene glycol)-modified adenosine deaminase(PEG-ADA). In J. M. Harris and S. Zalipsky (Eds) Poly(ethylene glycol):Chemistry and Biological Applications. American Chemical Society,Washington, D.C., p 145-154; Olson et al., 1997, Preparation andcharacterization of poly(ethylene glycol)ylated human growth hormoneantagonist. In J. M. Harris and S. Zalipsky (Eds) Poly(ethylene glycol):Chemistry and Biological Applications. American Chemical Society,Washington, D.C., p 170-181).

A peptide of the invention may be synthesized by conventionaltechniques. For example, the peptides of the invention may besynthesized by chemical synthesis using solid phase peptide synthesis.These methods employ either solid or solution phase synthesis methods(see for example, J. M. Stewart, and J. D. Young, Solid Phase PeptideSynthesis, 2^(nd) Ed., Pierce Chemical Co., Rockford Ill. (1984) and G.Barany and R. B. Merrifield, The Peptides: Analysis Synthesis, Biologyeditors E. Gross and J. Meienhofer Vol. 2 Academic Press, New York,1980, pp. 3-254 for solid phase synthesis techniques; and M Bodansky,Principles of Peptide Synthesis, Springer-Verlag, Berlin 1984, and E.Gross and J. Meienhofer, Eds., The Peptides: Analysis, Synthesis,Biology, suprs, Vol 1, for classical solution synthesis.)

The peptides may be chemically synthesized by Merrifield-type solidphase peptide synthesis. This method may be routinely performed to yieldpeptides up to about 60-70 residues in length, and may, in some cases,be utilized to make peptides up to about 100 amino acids long. Largerpeptides may also be generated synthetically via fragment condensationor native chemical ligation (Dawson et al., 2000, Ann. Rev. Biochem.69:923-960). An advantage to the utilization of a synthetic peptideroute is the ability to produce large amounts of peptides, even thosethat rarely occur naturally, with relatively high purities, i.e.,purities sufficient for research, diagnostic or therapeutic purposes.

Solid phase peptide synthesis is described by Stewart et al. in SolidPhase Peptide Synthesis, 2nd Edition, 1984, Pierce Chemical Company,Rockford, Ill.; and Bodanszky and Bodanszky in The Practice of PeptideSynthesis, 1984, Springer-Verlag, New York. At the outset, a suitablyprotected amino acid residue is attached through its carboxyl group to aderivatized, insoluble polymeric support, such as cross-linkedpolystyrene or polyamide resin. “Suitably protected” refers to thepresence of protecting groups on both the alpha-amino group of the aminoacid, and on any side chain functional groups. Side chain protectinggroups are generally stable to the solvents, reagents and reactionconditions used throughout the synthesis, and are removable underconditions which will not affect the final peptide product. Stepwisesynthesis of the oligopeptide is carried out by the removal of theN-protecting group from the initial amino acid, and coupling thereto ofthe carboxyl end of the next amino acid in the sequence of the desiredpeptide. This amino acid is also suitably protected. The carboxyl of theincoming amino acid can be activated to react with the N-terminus of thesupport-bound amino acid by formation into a reactive group, such asformation into a carbodiimide, a symmetric acid anhydride, or an “activeester” group, such as hydroxybenzotriazole or pentafluorophenyl esters.

Examples of solid phase peptide synthesis methods include the BOC methodwhich utilized tert-butyloxcarbonyl as the alpha-amino protecting group,and the FMOC method which utilizes 9-fluorenylmethyloxcarbonyl toprotect the alpha-amino of the amino acid residues, both which methodsare well-known by those of skill in the art.

Incorporation of N- and/or C-blocking groups may also be achieved usingprotocols conventional to solid phase peptide synthesis methods. Forincorporation of C-terminal blocking groups, for example, synthesis ofthe desired peptide is typically performed using, as solid phase, asupporting resin that has been chemically modified so that cleavage fromthe resin results in a peptide having the desired C-terminal blockinggroup. To provide peptides in which the C-terminus bears a primary aminoblocking group, for instance, synthesis is performed using ap-methylbenzhydrylamine (MBHA) resin, so that, when peptide synthesis iscompleted, treatment with hydrofluoric acid releases the desiredC-terminally amidated peptide. Similarly, incorporation of anN-methylamine blocking group at the C-terminus is achieved usingN-methylaminoethyl-derivatized DVB, resin, which upon HF treatmentreleases a peptide bearing an N-methylamidated C-terminus. Blockage ofthe C-terminus by esterification can also be achieved using conventionalprocedures. This entails use of resin/blocking group combination thatpermits release of side-chain peptide from the resin, to allow forsubsequent reaction with the desired alcohol, to form the esterfunction. FMOC protecting group, in combination with DVB resinderivatized with methoxyalkoxybenzyl alcohol or equivalent linker, canbe used for this purpose, with cleavage from the support being effectedby TFA in dicholoromethane. Esterification of the suitably activatedcarboxyl function, e.g. with DCC, can then proceed by addition of thedesired alcohol, followed by de-protection and isolation of theesterified peptide product.

The peptides of the invention may be prepared by standard chemical orbiological means of peptide synthesis. Biological methods include,without limitation, expression of a nucleic acid encoding a peptide in ahost cell or in an in vitro translation system.

Included in the invention are nucleic acid sequences that encode thepeptide of the invention. In one embodiment, the invention includesnucleic acid sequences encoding the amino acid sequence of one or moreTRIM proteins or one or more STUbLs. Accordingly, subclones of a nucleicacid sequence encoding a peptide of the invention can be produced usingconventional molecular genetic manipulation for subcloning genefragments, such as described by Sambrook et al., Molecular Cloning: ALaboratory Manual, Cold Springs Laboratory, Cold Springs Harbor, NewYork (2012), and Ausubel et al. (ed.), Current Protocols in MolecularBiology, John Wiley & Sons (New York, NY) (1999 and preceding editions),each of which is hereby incorporated by reference in its entirety. Thesubclones then are expressed in vitro or in vivo in bacterial cells toyield a smaller protein or polypeptide that can be tested for aparticular activity.

Combined with certain formulations, such peptides can be effectiveintracellular agents. However, in order to increase the efficacy of suchpeptides, the one or more peptides of the invention can be provided afusion peptide along with a second peptide which promotes“transcytosis”, e.g., uptake of the peptide by cells. For example, inone embodiment, the peptide may comprise a cell-penetrating domain, forexample a cell-penetrating peptide (CPP) to allow for the peptide toenter a cell. In one embodiment, the CPP is derived from HIV Tat.

To illustrate, the one or more peptides of the present invention can beprovided as part of a fusion polypeptide with all or a fragment of theN-terminal domain of the HIV protein Tat, e.g., residues 1-72 of Tat ora smaller fragment thereof which can promote transcytosis. In oneembodiment, the peptide comprises the protein transduction domain of HIVTat (YGRKKRRQRRR; (SEQ ID NO: 163)). In other embodiments, the one ormore peptides can be provided a fusion polypeptide with all or a portionof the antenopedia III protein. Other cell-penetrating domains thatmediate uptake of the peptide are known in the art, and are equallyapplicable for use in a fusion peptide of the present invention.

Nucleic Acids

In one embodiment, the composition of the invention comprises one orisolated nucleic acids. For example, in one embodiment, the one or moreisolated nucleic acids encodes one or more TRIM proteins. For example,in one embodiment, the one or more isolated nucleic acids encodes one ormore of human TRIM3, TRIM4, TRIM5, TRIM6, TRIM7, TRIM9, TRIM11, TRIM13,TRIM14, TRIM15, TRIM16, TRIM17, TRIM19 (also referred to herein as“PML”), TRIM20, TRIM21, TRIM24, TRIM25, TRIM27, TRIM28, TRIM29, TRIM32,TRIM34, TRIM39, TRIM43, TRIM44, TRIM45, TRIM46, TRIM49, TRIM50, TRIM52,TRIM58, TRIM59, TRIM65, TRIM67, TRIM69, TRIM70, TRIM74 and TRIM75; andmouse TRIM30. In certain embodiments, the one or more isolated nucleicacids encodes one or more STUbLs. For example, in one embodiment, theone or more isolated nucleic acids encodes one or more of RNF4 andRNF111 (Arkadia).

Exemplary nucleotide sequences encoding TRIM proteins is found in Table1.

In certain embodiments, a peptide corresponding to one or more TRIMproteins or one or more STUbLs is expressed from the one or more nucleicacids in a cell in vivo or in vitro using known techniques.

The nucleotide sequence of the isolated nucleic acids include both theDNA sequence that is transcribed into RNA and the RNA sequence that istranslated into a polypeptide. According to other embodiments, thenucleotide sequences are inferred from the amino acid sequence of thepeptides of the invention. As is known in the art several alternativenucleotide sequences are possible due to redundant codons, whileretaining the biological activity of the translated peptides.

Further, the invention encompasses an isolated nucleic acid comprising anucleotide sequence having substantial homology to a nucleotide sequenceencoding a disclosed herein. Preferably, the nucleotide sequence of anisolated nucleic acid is “substantially homologous,” that is, is about60% homologous, more preferably about 70% homologous, even morepreferably about 80% homologous, more preferably about 90% homologous,even more preferably, about 95% homologous, and even more preferablyabout 99% homologous to a nucleotide sequence of an isolated nucleicacid encoding a peptide of the invention.

In one embodiment, the composition comprises a combination of thenucleic acid molecules described herein. For example, in certainembodiments, the composition comprises an isolated nucleic acid moleculeencoding one or more TRIM proteins and an isolated nucleic acid moleculeencoding one or more STUbLs. In one embodiment, the compositioncomprises an isolated nucleic acid molecule encoding one or more TRIMproteins and one or more STUbLs.

Thus, the invention encompasses expression vectors and methods for theintroduction of exogenous DNA into cells with concomitant expression ofthe exogenous DNA in the cells such as those described, for example, inSambrook et al. (2012, Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Laboratory, New York), and in Ausubel et al. (1997,Current Protocols in Molecular Biology, John Wiley & Sons, New York).

The desired nucleic acid encoding one or more one or more TRIM proteinsor one or more STUbLs can be cloned into a number of types of vectors.However, the present invention should not be construed to be limited toany particular vector. Instead, the present invention should beconstrued to encompass a wide plethora of vectors which are readilyavailable and/or well-known in the art. For example, a desiredpolynucleotide of the invention can be cloned into a vector including,but not limited to a plasmid, a phagemid, a phage derivative, an animalvirus, and a cosmid. Vectors of particular interest include expressionvectors, replication vectors, probe generation vectors, and sequencingvectors.

In specific embodiments, the expression vector is selected from thegroup consisting of a viral vector, a bacterial vector and a mammaliancell vector. Numerous expression vector systems exist that comprise atleast a part or all of the compositions discussed above. Prokaryote-and/or eukaryote-vector based systems can be employed for use with thepresent invention to produce polynucleotides, or their cognatepolypeptides. Many such systems are commercially and widely available.

Further, the expression vector may be provided to a cell in the form ofa viral vector. Viral vector technology is well known in the art and isdescribed, for example, in Sambrook et al. (2012), and in Ausubel et al.(1997), and in other virology and molecular biology manuals. Viruses,which are useful as vectors include, but are not limited to,retroviruses, adenoviruses, adeno-associated viruses, herpes viruses,and lentiviruses. In general, a suitable vector contains an origin ofreplication functional in at least one organism, a promoter sequence,convenient restriction endonuclease sites, and one or more selectablemarkers. (See, e.g., WO 01/96584; WO 01/29058; and U.S. Pat. No.6,326,193.

A number of viral based systems have been developed for gene transferinto mammalian cells. For example, retroviruses provide a convenientplatform for gene delivery systems. A selected gene can be inserted intoa vector and packaged in retroviral particles using techniques known inthe art. The recombinant virus can then be isolated and delivered tocells of the subject either in vivo or ex vivo. A number of retroviralsystems are known in the art. In some embodiments, adenovirus vectorsare used. A number of adenovirus vectors are known in the art. In oneembodiment, lentivirus vectors are used.

For example, vectors derived from retroviruses such as the lentivirusare suitable tools to achieve long-term gene transfer since they allowlong-term, stable integration of a transgene and its propagation indaughter cells. Lentiviral vectors have the added advantage over vectorsderived from onco-retroviruses such as murine leukemia viruses in thatthey can transduce non-proliferating cells, such as hepatocytes. Theyalso have the added advantage of low immunogenicity. In a preferredembodiment, the composition includes a vector derived from anadeno-associated virus (AAV). Adeno-associated viral (AAV) vectors havebecome powerful gene delivery tools for the treatment of variousdisorders. AAV vectors possess a number of features that render themideally suited for gene therapy, including a lack of pathogenicity,minimal immunogenicity, and the ability to transduce postmitotic cellsin a stable and efficient manner. Expression of a particular genecontained within an AAV vector can be specifically targeted to one ormore types of cells by choosing the appropriate combination of AAVserotype, promoter, and delivery method

In one embodiment, the encoding sequence is contained within an AAVvector. More than 30 naturally occurring serotypes of AAV are available.Many natural variants in the AAV capsid exist, allowing identificationand use of an AAV with properties specifically suited for skeletalmuscle. AAV viruses may be engineered using conventional molecularbiology techniques, making it possible to optimize these particles forcell specific delivery of nucleic acid sequences, for minimizingimmunogenicity, for tuning stability and particle lifetime, forefficient degradation, for accurate delivery to the nucleus, etc.

Thus, expression of one or more TRIM proteins or one or more STUbLs canbe achieved by delivering a recombinantly engineered AAV or artificialAAV that contains one or more encoding sequences. The use of AAVs is acommon mode of exogenous delivery of DNA as it is relatively non-toxic,provides efficient gene transfer, and can be easily optimized forspecific purposes. Exemplary AAV serotypes include, but is not limitedto AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8 and AAV9.

Desirable AAV fragments for assembly into vectors include the capproteins, including the vp1, vp2, vp3 and hypervariable regions, the repproteins, including rep 78, rep 68, rep 52, and rep 40, and thesequences encoding these proteins. These fragments may be readilyutilized in a variety of vector systems and host cells. Such fragmentsmay be used alone, in combination with other AAV serotype sequences orfragments, or in combination with elements from other AAV or non-AAVviral sequences. As used herein, artificial AAV serotypes include,without limitation, AAV with a non-naturally occurring capsid protein.Such an artificial capsid may be generated by any suitable technique,using a selected AAV sequence (e.g., a fragment of a vp1 capsid protein)in combination with heterologous sequences which may be obtained from adifferent selected AAV serotype, non-contiguous portions of the same AAVserotype, from a non-AAV viral source, or from a non-viral source. Anartificial AAV serotype may be, without limitation, a chimeric AAVcapsid, a recombinant AAV capsid, or a “humanized” AAV capsid. Thusexemplary AAVs, or artificial AAVs, suitable for expression of one ormore TRIM proteins or one or more STUbLs, include AAV2/8 (see U.S. Pat.No. 7,282,199), AAV2/5 (available from the National Institutes ofHealth), AAV2/9 (International Patent Publication No. WO2005/033321),AAV2/6 (U.S. Pat. No. 6,156,303), and AAVrh8 (International PatentPublication No. WO2003/042397), among others.

For expression of the desired polynucleotide, at least one module ineach promoter functions to position the start site for RNA synthesis.The best known example of this is the TATA box, but in some promoterslacking a TATA box, such as the promoter for the mammalian terminaldeoxynucleotidyl transferase gene and the promoter for the SV40 genes, adiscrete element overlying the start site itself helps to fix the placeof initiation.

Additional promoter elements, i.e., enhancers, regulate the frequency oftranscriptional initiation. Typically, these are located in the region30-110 bp upstream of the start site, although a number of promotershave recently been shown to contain functional elements downstream ofthe start site as well. The spacing between promoter elements frequentlyis flexible, so that promoter function is preserved when elements areinverted or moved relative to one another. In the thymidine kinase (tk)promoter, the spacing between promoter elements can be increased to 50bp apart before activity begins to decline. Depending on the promoter,it appears that individual elements can function either co-operativelyor independently to activate transcription.

A promoter may be one naturally associated with a gene or polynucleotidesequence, as may be obtained by isolating the 5′ non-coding sequenceslocated upstream of the coding segment and/or exon. Such a promoter canbe referred to as “endogenous.” Similarly, an enhancer may be onenaturally associated with a polynucleotide sequence, located eitherdownstream or upstream of that sequence. Alternatively, certainadvantages will be gained by positioning the coding polynucleotidesegment under the control of a recombinant or heterologous promoter,which refers to a promoter that is not normally associated with apolynucleotide sequence in its natural environment. A recombinant orheterologous enhancer refers also to an enhancer not normally associatedwith a polynucleotide sequence in its natural environment. Suchpromoters or enhancers may include promoters or enhancers of othergenes, and promoters or enhancers isolated from any other prokaryotic,viral, or eukaryotic cell, and promoters or enhancers not “naturallyoccurring,” i.e., containing different elements of differenttranscriptional regulatory regions, and/or mutations that alterexpression. In addition to producing nucleic acid sequences of promotersand enhancers synthetically, sequences may be produced using recombinantcloning and/or nucleic acid amplification technology, including PCR™, inconnection with the compositions disclosed herein (U.S. Pat. Nos.4,683,202, 5,928,906). Furthermore, it is contemplated the controlsequences that direct transcription and/or expression of sequenceswithin non-nuclear organelles such as mitochondria, chloroplasts, andthe like, can be employed as well.

Naturally, it will be important to employ a promoter and/or enhancerthat effectively directs the expression of the DNA segment in the celltype, organelle, and organism chosen for expression. Those of skill inthe art of molecular biology generally know how to use promoters,enhancers, and cell type combinations for protein expression, forexample, see Sambrook et al. (2012). The promoters employed may beconstitutive, tissue-specific, inducible, and/or useful under theappropriate conditions to direct high level expression of the introducedDNA segment, such as is advantageous in the large-scale production ofrecombinant proteins and/or peptides. The promoter may be heterologousor endogenous.

In one embodiment, the promoter or enhancer specifically directsexpression of the one or more TRIM proteins or one or more STUbLs in theintestinal epithelium in neural tissue. For example, in certainembodiments, the promoter or enhancer specifically directs expression ofthe one or more TRIM proteins or one or more STUbLs in a neuron,astrocyte, oligodendrocyte, Perkinje cell, pyramidal cell, or the like.

In order to assess the expression of the desired polynucleotide, theexpression vector to be introduced into a cell can also contain either aselectable marker gene or a reporter gene or both to facilitateidentification and selection of expressing cells from the population ofcells sought to be transfected or infected through viral vectors. Inother embodiments, the selectable marker may be carried on a separatepiece of DNA and used in a co-transfection procedure. Both selectablemarkers and reporter genes may be flanked with appropriate regulatorysequences to enable expression in the host cells. Useful selectablemarkers are known in the art and include, for example,antibiotic-resistance genes, such as neo and the like.

Reporter genes are used for identifying potentially transfected cellsand for evaluating the functionality of regulatory sequences. Reportergenes that encode for easily assayable proteins are well known in theart. In general, a reporter gene is a gene that is not present in orexpressed by the recipient organism or tissue and that encodes a proteinwhose expression is manifested by some easily detectable property, e.g.,enzymatic activity. Expression of the reporter gene is assayed at asuitable time after the DNA has been introduced into the recipientcells.

Suitable reporter genes may include genes encoding luciferase,beta-galactosidase, chloramphenicol acetyl transferase, secretedalkaline phosphatase, or the green fluorescent protein gene (see, e.g.,Ui-Tei et al., 2000 FEBS Lett. 479:79-82). Suitable expression systemsare well known and may be prepared using well known techniques orobtained commercially. Internal deletion constructs may be generatedusing unique internal restriction sites or by partial digestion ofnon-unique restriction sites. Constructs may then be transfected intocells that display high levels of siRNA polynucleotide and/orpolypeptide expression. In general, the construct with the minimal 5′flanking region showing the highest level of expression of reporter geneis identified as the promoter. Such promoter regions may be linked to areporter gene and used to evaluate agents for the ability to modulatepromoter-driven transcription.

In the context of an expression vector, the vector can be readilyintroduced into a host cell, e.g., mammalian, bacterial, yeast or insectcell by any method in the art. For example, the expression vector can betransferred into a host cell by physical, chemical or biological means.

Physical methods for introducing a polynucleotide into a host cellinclude calcium phosphate precipitation, lipofection, particlebombardment, microinjection, electroporation, and the like. Methods forproducing cells comprising vectors and/or exogenous nucleic acids arewell-known in the art. See, for example, Sambrook et al. (2012,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory,New York), and in Ausubel et al. (1997, Current Protocols in MolecularBiology, John Wiley & Sons, New York).

Biological methods for introducing a polynucleotide of interest into ahost cell include the use of DNA and RNA vectors. Viral vectors, andespecially retroviral vectors, have become the most widely used methodfor inserting genes into mammalian, e.g., human cells. Other viralvectors can be derived from lentivirus, poxviruses, herpes simplex virusI, adenoviruses and adeno-associated viruses, and the like. See, forexample, U.S. Pat. Nos. 5,350,674 and 5,585,362.

Chemical means for introducing a polynucleotide into a host cell includecolloidal dispersion systems, such as macromolecule complexes,nanocapsules, microspheres, beads, and lipid-based systems includingoil-in-water emulsions, micelles, mixed micelles, and liposomes. Apreferred colloidal system for use as a delivery vehicle in vitro and invivo is a liposome (i.e., an artificial membrane vesicle). Thepreparation and use of such systems is well known in the art.

Regardless of the method used to introduce exogenous nucleic acids intoa host cell, in order to confirm the presence of the recombinant DNAsequence in the host cell, a variety of assays may be performed. Suchassays include, for example, “molecular biological” assays well known tothose of skill in the art, such as Southern and Northern blotting,RT-PCR and PCR; “biochemical” assays, such as detecting the presence orabsence of a particular peptide, e.g., by immunological means (ELISAsand Western blots) or by assays described herein to identify agentsfalling within the scope of the invention.

Any DNA vector or delivery vehicle can be utilized to transfer thedesired polynucleotide to a cell in vitro or in vivo. In the case wherea non-viral delivery system is utilized, a preferred delivery vehicle isa liposome. The above-mentioned delivery systems and protocols thereforecan be found in Gene Targeting Protocols, 2ed., pp 1-35 (2002) and GeneTransfer and Expression Protocols, Vol. 7, Murray ed., pp 81-89 (1991).

“Liposome” is a generic term encompassing a variety of single andmultilamellar lipid vehicles formed by the generation of enclosed lipidbilayers or aggregates. Liposomes may be characterized as havingvesicular structures with a phospholipid bilayer membrane and an inneraqueous medium. Multilamellar liposomes have multiple lipid layersseparated by aqueous medium. They form spontaneously when phospholipidsare suspended in an excess of aqueous solution. The lipid componentsundergo self-rearrangement before the formation of closed structures andentrap water and dissolved solutes between the lipid bilayers. However,the present invention also encompasses compositions that have differentstructures in solution than the normal vesicular structure. For example,the lipids may assume a micellar structure or merely exist as nonuniformaggregates of lipid molecules. Also contemplated arelipofectamine-nucleic acid complexes.

In one embodiment, the composition of the invention comprises in vitrotranscribed (IVT) RNA encoding one or more components of the one or moreTRIM proteins or one or more STUbLs. In one embodiment, an IVT RNA canbe introduced to a cell as a form of transient transfection. The RNA isproduced by in vitro transcription using a plasmid DNA templategenerated synthetically. DNA of interest from any source can be directlyconverted by PCR into a template for in vitro mRNA synthesis usingappropriate primers and RNA polymerase. The source of the DNA can be,for example, genomic DNA, plasmid DNA, phage DNA, cDNA, synthetic DNAsequence or any other appropriate source of DNA. The desired templatefor in vitro transcription is one or more TRIM proteins or one or moreSTUbLs.

In one embodiment, the DNA to be used for PCR contains an open readingframe. The DNA can be from a naturally occurring DNA sequence from thegenome of an organism. In one embodiment, the DNA is a full length geneof interest of a portion of a gene. The gene can include some or all ofthe 5′ and/or 3′ untranslated regions (UTRs). The gene can include exonsand introns. In one embodiment, the DNA to be used for PCR is a humangene. In another embodiment, the DNA to be used for PCR is a human geneincluding the 5′ and 3′ UTRs. The DNA can alternatively be an artificialDNA sequence that is not normally expressed in a naturally occurringorganism. An exemplary artificial DNA sequence is one that containsportions of genes that are ligated together to form an open readingframe that encodes a fusion protein. The portions of DNA that areligated together can be from a single organism or from more than oneorganism.

In one embodiment, the composition of the present invention comprises amodified nucleic acid encoding one or more one or more TRIM proteins orRNF4 described herein. For example, in one embodiment, the compositioncomprises a nucleoside-modified RNA. In one embodiment, the compositioncomprises a nucleoside-modified mRNA. Nucleoside-modified mRNA haveparticular advantages over non-modified mRNA, including for example,increased stability, low immunogenicity, and enhanced translation.Nucleoside-modified mRNA useful in the present invention is furtherdescribed in U.S. Pat. No. 8,278,036, which is incorporated by referenceherein in its entirety.

Modified Cell

The present invention includes a composition comprising a cell whichcomprises one or more TRIM proteins, one or more STUbLs, a nucleic acidencoding a one or more TRIM proteins, a nucleic acid encoding a one ormore STUbLs or a combination thereof. In one embodiment, the cell isgenetically modified to express a protein and/or nucleic acid of theinvention. In certain embodiments, genetically modified cell isautologous to a subject being treated with the composition of theinvention. Alternatively, the cells can be allogeneic, syngeneic, orxenogeneic with respect to the subject. In certain embodiment, the cellis able to secrete or release the expressed protein into extracellularspace in order to deliver the peptide to one or more other cells.

The genetically modified cell may be modified in vivo or ex vivo, usingtechniques standard in the art. Genetic modification of the cell may becarried out using an expression vector or using a naked isolated nucleicacid construct.

In one embodiment, the cell is obtained and modified ex vivo, using anisolated nucleic acid encoding one or more proteins described herein. Inone embodiment, the cell is obtained from a subject, geneticallymodified to express the protein and/or nucleic acid, and isre-administered to the subject. In certain embodiments, the cell isexpanded ex vivo or in vitro to produce a population of cells, whereinat least a portion of the population is administered to a subject inneed.

In one embodiment, the cell is genetically modified to stably expressthe protein. In another embodiment, the cell is genetically modified totransiently express the protein.

Substrates

The present invention provides a scaffold or substrate compositioncomprising a protein of the invention, an isolated nucleic acid of theinvention, a cell expressing the protein of the invention, or acombination thereof. For example, in one embodiment, a protein of theinvention, an isolated nucleic acid of the invention, a cell a cellexpressing the protein of the invention, or a combination thereof isincorporated within a scaffold. In another embodiment, a protein of theinvention, an isolated nucleic acid of the invention, a cell expressingthe protein of the invention, or a combination thereof is applied to thesurface of a scaffold. The scaffold of the invention may be of any typeknown in the art. Non-limiting examples of such a scaffold includes a,hydrogel, electrospun scaffold, foam, mesh, sheet, patch, and sponge.

Therapeutic Methods

The present invention also provides therapeutic methods for a disease ordisorder associated with protein misfolding, protein aggregates, or acombination thereof.

In various embodiments, diseases and disorders treatable by the methodsof the invention include, but are not limited to: polyQ disorders suchas SCA1, SCA2, SCA3, SCA6, SCA7, SCA17, Huntington's disease,Dentatorubral-pallidoluysian atrophy (DRPLA), Alzheimer's disease,Parkinson's disease, amyotrophic lateral sclerosis (ALS), transmissiblespongiform encephalopathies (prion disease), tauopathies, Frontotemporallobar degeneration (FTLD), AL amyloidosis, AA amyloidosis, FamilialMediterranean fever, senile systemic amyloidosis, familial amyloidoticpolyneuropathy, hemodialysis-related amyloidosis, ApoAI amyloidosis,ApoAII amyloidosis, ApoAIV amyloidosis, Finnish hereditary amyloidosis,lysozyme amyloidosis, fibrinogen amyloidosis, Icelandic hereditarycerebral amyloid angiopathy, type II diabetes, medullary carcinoma ofthe thyroid, atrial amyloidosis, hereditary cerebral hemorrhage withamyloidosis, pituitary prolactinoma, injection-localized amyloidosis,aortic medial amyloidosis, hereditary lattice corneal dystrophy, cornealamyloidosis associated with trichiasis, cataract, calcifying epithelialodontogenic tumor, pulmonary alveolar proteinosis, inclusion-bodymyostis, and cuteaneous lichen amyloidosis. In certain embodiments, themethod comprises the treatment or prevention of cancer associated withp53 mutant aggregates, including but not limited to bladder carcinoma,astrocytoma, pharynx carcinoma, lymphoma, and adenocarcinoma.

It will be appreciated by one of skill in the art, when armed with thepresent disclosure including the methods detailed herein, that theinvention is not limited to treatment of a disease associated withprotein misfolding or protein aggregates that is already established.Particularly, the disease or disorder need not have manifested to thepoint of detriment to the subject; indeed, the disease or disorder neednot be detected in a subject before treatment is administered. That is,significant signs or symptoms of the disease or disorder do not have tooccur before the present invention may provide benefit. Therefore, thepresent invention includes a method for preventing a disease or disorderassociated with protein misfolding or protein aggregates, in that amodulator composition, as discussed previously elsewhere herein, can beadministered to a subject prior to the onset of the disease or disorder,thereby preventing the disease or disorder.

One of skill in the art, when armed with the disclosure herein, wouldappreciate that the prevention of a disease associated with proteinmisfolding or protein aggregates, encompasses administering to a subjecta modulator composition as a preventative measure against thedevelopment of, or progression of a disease associated with proteinmisfolding or protein aggregates. As more fully discussed elsewhereherein, methods of modulating the level or activity of a gene, or geneproduct, encompass a wide plethora of techniques for modulating not onlythe level and activity of polypeptide gene products, but also formodulating expression of a nucleic acid, including either transcription,translation, or both.

Additionally, as disclosed elsewhere herein, one skilled in the artwould understand, once armed with the teaching provided herein, that thepresent invention encompasses methods of treating, or preventing, a widevariety of diseases associated with protein misfolding or proteinaggregates, where modulating the level or activity of a gene, or geneproduct treats or prevents the disease. Various methods for assessingwhether a disease is associated protein misfolding or protein aggregatesare known in the art. Further, the invention encompasses treatment orprevention of such diseases discovered in the future.

In one aspect, the method comprises use of one or more TRIM proteins tostabilize a misfolded protein. In certain aspects, stabilization of afunctional misfolded protein via one or more TRIM proteins describedherein can treat or prevent a disease or disorder associated with themisfolded protein. For example, in one embodiment, stabilization ofmutant cystic fibrosis transmembrane conductance regulator (CFTR), viaone or more TRIM proteins described herein, would allow mutant CFTR tofunction instead of being degraded. It is envisioned that using TRIMproteins to stabilize misfolded proteins can be used to treat cysticfibrosis and other diseases associated with degradation of partiallyfunctional proteins. Stabilization of proteins, via one or more TRIMproteins described herein, can be used to treat any disease or disorderassociated with degradation of functional mutant protein, including butnot limited to cystic fibrosis and lysosomal storage diseases such asGaucher's disease and Fabry's disease.

The invention encompasses administration of a modulator of a gene, orgene product. To practice the methods of the invention; the skilledartisan would understand, based on the disclosure provided herein, howto formulate and administer the appropriate modulator composition to asubject. The present invention is not limited to any particular methodof administration or treatment regimen.

In one embodiment, the method comprises administering to the subject inneed an effective amount of a composition that increases the expressionor activity of one or more TRIM protein or one or more STUbLs.

For example, in one embodiment, the method comprises administering tothe subject in need an effective amount of a composition that increasesthe expression or activity of one or more of human TRIM3, TRIM4, TRIM5,TRIM6, TRIM7, TRIM9, TRIM11, TRIM13, TRIM14, TRIM15, TRIM16, TRIM17,TRIM19 (also referred to herein as “PML”), TRIM20, TRIM21, TRIM24,TRIM25, TRIM27, TRIM28, TRIM29, TRIM32, TRIM34, TRIM39, TRIM43, TRIM44,TRIM45, TRIM46, TRIM49, TRIM50, TRIM52, TRIM58, TRIM59, TRIM65, TRIM67,TRIM69, TRIM70, TRIM74 and TRIM75; and mouse TRIM30.

In one embodiment, the method comprises administering to the subject inneed an effective amount of a composition that increases the expressionor activity of one or more of RNF4 and RNF111 (Arkadia).

In one embodiment, the method comprises administering to the subject aneffective amount of a composition that increases the expression oractivity of one or more TRIM proteins and one or more STUbLs.

In one embodiment, the method comprises increasing the expression oractivity of the one or more TRIM proteins or one or more STUbLs in atleast one neural cell of the subject. For example, in certainembodiments, the method comprises increasing the expression or activityof the one or more TRIM proteins or one or more STUbLs in a at least oneneuron, astrocyte, oligodendrocyte, Perkinje cell, pyramidal cell, orthe like.

In one embodiment, the method comprises contacting the neural tissue ofa subject with an effective amount of a composition that increases theexpression or activity of one or more components of the one or more TRIMproteins or one or more STUbLs. For example, in certain embodiments, themethod comprises contacting a neuron, astrocyte, oligodendrocyte,Perkinje cell, pyramidal cell, or the like, of a subject with aneffective amount of a composition that increases the expression oractivity of one or more TRIM proteins or one or more STUbLs.

One of skill in the art will appreciate that the modulators of theinvention can be administered singly or in any combination. Further, themodulators of the invention can be administered singly or in anycombination in a temporal sense, in that they may be administeredconcurrently, or before, and/or after each other. One of ordinary skillin the art will appreciate, based on the disclosure provided herein,that the modulator compositions of the invention can be used to preventor to treat a disease or disorder associated with a misfolded protein orprotein aggregate, and that a modulator composition can be used alone orin any combination with another modulator to effect a prophylactic ortherapeutic result.

In various embodiments, any of the modulators of the invention describedherein can be administered alone or in combination with other modulatorsof other molecules associated with a disease associated with proteinmisfolding or protein aggregates. In various embodiments, any of themodulators of the invention described herein can be administered aloneor in combination with other therapeutic or preventative agents whichmay be used to treat or prevent a disease associated with proteinmisfolding or protein aggregates. Exemplary therapeutic agents which maybe used in combination with the modulators of the present inventioninclude, but is not limited to, anti-amyloid-β antibodies and anti-tauantibodies.

Gene Therapy

Contacting cells in a subject with a nucleic acid composition thatencodes a protein that increases the expression or activity of one ormore TRIM proteins or one or more STUbLs can inhibit or delay the onsetof one or more symptoms of a disease or disorder associated with proteinmisfolding or protein aggregates.

In one embodiment, the nucleic acid composition of the present inventionencodes one or more peptides. For example, in one embodiment, a nucleicacid composition can encode a peptide that comprises an amino acidsequence of one or more TRIM proteins. For example, in one embodiment,the nucleic acid composition encodes a peptide comprising one or more ofhuman TRIM3, TRIM4, TRIM5, TRIM6, TRIM7, TRIM9, TRIM11, TRIM13, TRIM14,TRIM15, TRIM16, TRIM17, TRIM19 (also referred to herein as “PML”),TRIM20, TRIM21, TRIM24, TRIM25, TRIM27, TRIM28, TRIM29, TRIM32, TRIM34,TRIM39, TRIM43, TRIM44, TRIM45, TRIM46, TRIM49, TRIM50, TRIM52, TRIM58,TRIM59, TRIM65, TRIM67, TRIM69, TRIM70, TRIM74 and TRIM75; and mouseTRIM30. In certain embodiments, the nucleic acid composition encodes apeptide comprising the amino acid sequence of one or more STUbLs. Forexample, in one embodiment, the nucleic acid composition encodes apeptide comprising one or more of RNF4 and RNF111 (Arkadia).

The invention should also be construed to include any form of a nucleicacid encoding a peptide having substantial homology to the peptidesdisclosed herein. Preferably, a peptide which is “substantiallyhomologous” is about 50% homologous, more preferably about 70%homologous, even more preferably about 80% homologous, more preferablyabout 90% homologous, even more preferably, about 95% homologous, andeven more preferably about 99% homologous to amino acid sequence of thepeptides disclosed herein.

In one embodiment, the composition of the invention comprises a nucleicacid encoding a peptide, a fragment of a peptide, a homolog, a variant,a derivative or a salt of a peptide described herein. For example, incertain embodiments, the composition comprises a nucleic acid encoding apeptide comprising one or more TRIM proteins, a fragment of one or moreTRIM proteins, a homolog of one or more TRIM proteins, a variant of oneor more TRIM proteins, or a derivative of one or more TRIM proteins. Incertain embodiments, the composition comprises a nucleic acid encoding apeptide comprising one or more STUbLs, a fragment of one or more STUbLs,a homolog of one or more STUbLs, a variant of one or more STUbLs, or aderivative of one or more STUbLs.

According to the present invention, a method is also provided ofsupplying protein to a cell which carries a normal, or a mutant gene,associated with diminished or insufficient activity of one or more TRIMproteins or one or more STUbLs. Supplying protein to a cell with amutant gene should allow normal functioning of the recipient cells. Thenucleic acid encoding a peptide may be introduced into the cell in avector such that the nucleic acid remains extrachromosomal. In such asituation, the nucleic acid will be expressed by the cell from theextrachromosomal location. More preferred is the situation where thenucleic acid or a part thereof is introduced into the cell in such a waythat it integrates into the cell's genome or recombines with theendogenous mutant gene present in the cell. Vectors for introduction ofgenes both for recombination, for integration, and for extrachromosomalmaintenance are known in the art, and any suitable vector may be used.Methods for introducing DNA into cells such as electroporation, calciumphosphate co-precipitation and viral transduction are known in the art,and the choice of method is within the competence of the practitioner.

As generally discussed above, a nucleic acid, where applicable, may beemployed in gene therapy methods in order to increase the level oractivity of the peptides of the invention even in those persons in whichthe wild type gene is expressed at a “normal” level, but the geneproduct is insufficiently functional.

“Gene therapy” includes both conventional gene therapy where a lastingeffect is achieved by a single treatment, and the administration of genetherapeutic agents, which involves the one time or repeatedadministration of a therapeutically effective DNA or mRNA.Oligonucleotides can be modified to enhance their uptake, e.g., bysubstituting their negatively charged phosphodiester groups by unchargedgroups. One or more TRIM proteins or one or more STUbLs of the presentinvention can be delivered using gene therapy methods, for examplelocally in neural cell or tissue or systemically (e.g., via vectors thatselectively target specific tissue types, for example, tissue-specificadeno-associated viral vectors). In some embodiments, primary cellsharvested from the individual can be transfected ex vivo with a nucleicacid encoding any of the peptides of the present invention, and thenreturned the transfected cells to the individual's body.

Gene therapy methods are well known in the art. See, e.g., WO96/07321which discloses the use of gene therapy methods to generateintracellular antibodies. Gene therapy methods have also beensuccessfully demonstrated in human patients. See, e.g., Baumgartner etal., Circulation 97: 12, 1114-1123 (1998), Fatham, C. G. ‘A gene therapyapproach to treatment of autoimmune diseases’, Immun. Res. 18:15-26(2007); and U.S. Pat. No. 7,378,089, both incorporated herein byreference. See also Bainbridge J W B et al. “Effect of gene therapy onvisual function in Leber's congenital Amaurosis”. N Engl J Med358:2231-2239, 2008; and Maguire A M et al. “Safety and efficacy of genetransfer for Leber's Congenital Amaurosis”. N Engl J Med 358:2240-8,2008.

There are two major approaches for introducing a nucleic acid encoding apeptide or protein (optionally contained in a vector) into a patientscells; in vivo and ex vivo. For in vivo delivery, in certain instances,the nucleic acid is injected directly into the patient, sometimes at thesite where the protein is most required. For ex vivo treatment, thepatient's cells are removed, the nucleic acid is introduced into theseisolated cells and the modified cells are administered to the patienteither directly or, for example, encapsulated within porous membraneswhich are implanted into the patient (see, e.g., U.S. Pat. Nos.4,892,538 and 5,283,187). There are a variety of techniques availablefor introducing nucleic acids into viable cells. The techniques varydepending upon whether the nucleic acid is transferred into culturedcells in vitro, or in vivo in the cells of the intended host. Techniquessuitable for the transfer of nucleic acid into mammalian cells in vitroinclude the use of liposomes, electroporation, microinjection, cellfusion, DEAE-dextran, the calcium phosphate precipitation method, etc.Commonly used vectors for ex vivo delivery of the gene are retroviraland lentiviral vectors.

Gene therapy would be carried out according to generally acceptedmethods, for example, as described by Friedman et al., 1991, Cell66:799-806 or Culver, 1996, Bone Marrow Transplant 3:S6-9; Culver, 1996,Mol. Med. Today 2:234-236. In one embodiment, cells from a patient wouldbe first analyzed by the diagnostic methods known in the art, toascertain the expression or activity of one or more TRIM proteins or oneor more STUbLs. A virus or plasmid vector, containing a copy of the geneor a functional equivalent thereof linked to expression control elementsand capable of replicating inside the cells, is prepared. The vector maybe capable of replicating inside the cells. Alternatively, the vectormay be replication deficient and is replicated in helper cells for usein gene therapy. Suitable vectors are known, such as disclosed in U.S.Pat. No. 5,252,479 and PCT published application WO 93/07282 and U.S.Pat. Nos. 5,691,198; 5,747,469; 5,436,146 and 5,753,500. The vector isthen injected into the patient. If the transfected gene is notpermanently incorporated into the genome of each of the targeted cells,the treatment may have to be repeated periodically.

Gene transfer systems known in the art may be useful in the practice ofthe gene therapy methods of the present invention. These include viraland nonviral transfer methods. A number of viruses have been used asgene transfer vectors or as the basis for repairing gene transfervectors, including papovaviruses (e.g., SV40, Madzak et al., 1992, J.Gen. Virol. 73:1533-1536), adenovirus (Berkner, 1992; Curr. TopicsMicrobiol. Immunol. 158:39-66), vaccinia virus (Moss, 1992, CurrentOpin. Biotechnol. 3:518-522; Moss, 1996, PNAS 93:11341-11348),adeno-associated virus (Russell and Hirata, 1998, Mol. Genetics18:325-330), herpesviruses including HSV and EBV (Fink et al., 1996,Ann. Rev. Neurosci. 19:265-287), lentiviruses (Naldini et al., 1996,PNAS 93:11382-11388), Sindbis and Semliki Forest virus (Berglund et al.,1993, Biotechnol. 11:916-920), and retroviruses of avian (Petropoulos etal., 1992, J. Virol. 66:3391-3397), murine (Miller, 1992, Hum. GeneTher. 3:619-624), and human origin (Shimada et al., 1991; Helseth etal., 1990; Page et al., 1990; Buchschacher and Panganiban, 1992, J.Virol. 66:2731-2739). Most human gene therapy protocols have been basedon disabled murine retroviruses, although adenovirus andadeno-associated virus are also being used.

Nonviral gene transfer methods known in the art include chemicaltechniques such as calcium phosphate coprecipitation; mechanicaltechniques, for example microinjection; membrane fusion-mediatedtransfer via liposomes; and direct DNA uptake and receptor-mediated DNAtransfer (Curiel et al., 1992, Am. J. Respir. Cell. Mol. Biol6:247-252). Viral-mediated gene transfer can be combined with direct invitro gene transfer using liposome delivery, allowing one to direct theviral vectors to the tumor cells and not into the surroundingnon-dividing cells. Injection of producer cells would then provide acontinuous source of vector particles. This technique has been approvedfor use in humans with inoperable brain tumors.

In an approach which combines biological and physical gene transfermethods, plasmid DNA of any size is combined with apolylysine-conjugated antibody specific to the adenovirus hexon protein,and the resulting complex is bound to an adenovirus vector. Thetrimolecular complex is then used to infect cells. The adenovirus vectorpermits efficient binding, internalization, and degradation of theendosome before the coupled DNA is damaged. For other techniques for thedelivery of adenovirus based vectors see U.S. Pat. Nos. 5,691,198;5,747,469; 5,436,146 and 5,753,500.

Liposome/DNA complexes have been shown to be capable of mediating directin vivo gene transfer. While in standard liposome preparations the genetransfer process is nonspecific, localized in vivo uptake and expressionhave been reported in tumor deposits, for example, following direct insitu administration.

Expression vectors in the context of gene therapy are meant to includethose constructs containing sequences sufficient to express apolynucleotide that has been cloned therein. In viral expressionvectors, the construct contains viral sequences sufficient to supportpackaging of the construct. If the polynucleotide encodes a protein,expression will produce the protein. If the polynucleotide encodes anantisense polynucleotide or a ribozyme, expression will produce theantisense polynucleotide or ribozyme. Thus in this context, expressiondoes not require that a protein product be synthesized. In addition tothe polynucleotide cloned into the expression vector, the vector alsocontains a promoter functional in eukaryotic cells. The clonedpolynucleotide sequence is under control of this promoter. Suitableeukaryotic promoters include those described above. The expressionvector may also include sequences, such as selectable markers and othersequences described herein.

In certain embodiments, the method comprises the use of gene transfertechniques which target an isolated nucleic acid directly to neuraltissue. Receptor-mediated gene transfer, for example, is accomplished bythe conjugation of a nucleic acid molecule (usually in the form ofcovalently closed supercoiled plasmid) to a protein ligand viapolylysine. Ligands are chosen on the basis of the presence of thecorresponding ligand receptors on the cell surface of the targetcell/tissue type. These ligand-DNA conjugates can be injected directlyinto the blood if desired and are directed to the target tissue wherereceptor binding and internalization of the DNA-protein complex occurs.To overcome the problem of intracellular destruction of DNA,co-infection with adenovirus can be included to disrupt endosomefunction.

Pharmaceutical Compositions and Formulations

The invention also encompasses the use of pharmaceutical compositions ofthe invention or salts thereof to practice the methods of the invention.Such a pharmaceutical composition may consist of at least one modulatorcomposition of the invention or a salt thereof in a form suitable foradministration to a subject, or the pharmaceutical composition maycomprise at least one modulator composition of the invention or a saltthereof, and one or more pharmaceutically acceptable carriers, one ormore additional ingredients, or some combination of these. The compoundor conjugate of the invention may be present in the pharmaceuticalcomposition in the form of a physiologically acceptable salt, such as incombination with a physiologically acceptable cation or anion, as iswell known in the art.

In one embodiment, the pharmaceutical compositions useful for practicingthe methods of the invention may be administered to deliver a dose ofbetween 1 ng/kg/day and 100 mg/kg/day. In another embodiment, thepharmaceutical compositions useful for practicing the invention may beadministered to deliver a dose of between 1 ng/kg/day and 500 mg/kg/day.

The relative amounts of the active ingredient, the pharmaceuticallyacceptable carrier, and any additional ingredients in a pharmaceuticalcomposition of the invention will vary, depending upon the identity,size, and condition of the subject treated and further depending uponthe route by which the composition is to be administered. By way ofexample, the composition may comprise between 0.1% and 100% (w/w) activeingredient.

Pharmaceutical compositions that are useful in the methods of theinvention may be suitably developed for oral, rectal, vaginal,parenteral, topical, pulmonary, intranasal, buccal, ophthalmic, oranother route of administration. A composition useful within the methodsof the invention may be directly administered to the skin, vagina or anyother tissue of a mammal. Other contemplated formulations includeliposomal preparations, resealed erythrocytes containing the activeingredient, and immunologically-based formulations. The route(s) ofadministration will be readily apparent to the skilled artisan and willdepend upon any number of factors including the type and severity of thedisease being treated, the type and age of the veterinary or humansubject being treated, and the like.

The formulations of the pharmaceutical compositions described herein maybe prepared by any method known or hereafter developed in the art ofpharmacology. In general, such preparatory methods include the step ofbringing the active ingredient into association with a carrier or one ormore other accessory ingredients, and then, if necessary or desirable,shaping or packaging the product into a desired single- or multi-doseunit.

As used herein, a “unit dose” is a discrete amount of the pharmaceuticalcomposition comprising a predetermined amount of the active ingredient.The amount of the active ingredient is generally equal to the dosage ofthe active ingredient that would be administered to a subject or aconvenient fraction of such a dosage such as, for example, one-half orone-third of such a dosage. The unit dosage form may be for a singledaily dose or one of multiple daily doses (e.g., about 1 to 4 or moretimes per day). When multiple daily doses are used, the unit dosage formmay be the same or different for each dose.

Although the descriptions of pharmaceutical compositions provided hereinare principally directed to pharmaceutical compositions that aresuitable for ethical administration to humans, it will be understood bythe skilled artisan that such compositions are generally suitable foradministration to animals of all sorts. Modification of pharmaceuticalcompositions suitable for administration to humans in order to renderthe compositions suitable for administration to various animals is wellunderstood, and the ordinarily skilled veterinary pharmacologist maydesign and perform such modification with merely ordinary, if any,experimentation. Subjects to which administration of the pharmaceuticalcompositions of the invention is contemplated include, but are notlimited to, humans and other primates, mammals including commerciallyrelevant mammals such as cattle, pigs, horses, sheep, cats, and dogs.

In one embodiment, the compositions of the invention are formulatedusing one or more pharmaceutically acceptable excipients or carriers. Inone embodiment, the pharmaceutical compositions of the inventioncomprise a therapeutically effective amount of a compound or conjugateof the invention and a pharmaceutically acceptable carrier.Pharmaceutically acceptable carriers that are useful, include, but arenot limited to, glycerol, water, saline, ethanol and otherpharmaceutically acceptable salt solutions such as phosphates and saltsof organic acids. Examples of these and other pharmaceuticallyacceptable carriers are described in Remington's Pharmaceutical Sciences(1991, Mack Publication Co., New Jersey).

The carrier may be a solvent or dispersion medium containing, forexample, water, ethanol, polyol (for example, glycerol, propyleneglycol, and liquid polyethylene glycol, and the like), suitable mixturesthereof, and vegetable oils. The proper fluidity may be maintained, forexample, by the use of a coating such as lecithin, by the maintenance ofthe required particle size in the case of dispersion and by the use ofsurfactants. Prevention of the action of microorganisms may be achievedby various antibacterial and antifungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, sodium chloride, or polyalcohols such as mannitol and sorbitol,in the composition. Prolonged absorption of the injectable compositionsmay be brought about by including in the composition an agent thatdelays absorption, for example, aluminum monostearate or gelatin. In oneembodiment, the pharmaceutically acceptable carrier is not DMSO alone.

Formulations may be employed in admixtures with conventional excipients,i.e., pharmaceutically acceptable organic or inorganic carriersubstances suitable for oral, vaginal, parenteral, nasal, intravenous,subcutaneous, enteral, or any other suitable mode of administration,known to the art. The pharmaceutical preparations may be sterilized andif desired mixed with auxiliary agents, e.g., lubricants, preservatives,stabilizers, wetting agents, emulsifiers, salts for influencing osmoticpressure buffers, coloring, flavoring and/or aromatic substances and thelike. They may also be combined where desired with other active agents,e.g., other analgesic agents.

As used herein, “additional ingredients” include, but are not limitedto, one or more of the following: excipients; surface active agents;dispersing agents; inert diluents; granulating and disintegratingagents; binding agents; lubricating agents; sweetening agents; flavoringagents; coloring agents; preservatives; physiologically degradablecompositions such as gelatin; aqueous vehicles and solvents; oilyvehicles and solvents; suspending agents; dispersing or wetting agents;emulsifying agents, demulcents; buffers; salts; thickening agents;fillers; emulsifying agents; antioxidants; antibiotics; antifungalagents; stabilizing agents; and pharmaceutically acceptable polymeric orhydrophobic materials. Other “additional ingredients” that may beincluded in the pharmaceutical compositions of the invention are knownin the art and described, for example in Genaro, ed. (1985, Remington'sPharmaceutical Sciences, Mack Publishing Co., Easton, PA), which isincorporated herein by reference.

The composition of the invention may comprise a preservative from about0.005% to 2.0% by total weight of the composition. The preservative isused to prevent spoilage in the case of exposure to contaminants in theenvironment. Examples of preservatives useful in accordance with theinvention included but are not limited to those selected from the groupconsisting of benzyl alcohol, sorbic acid, parabens, imidurea andcombinations thereof. A particularly preferred preservative is acombination of about 0.5% to 2.0% benzyl alcohol and 0.05% to 0.5%sorbic acid.

The composition preferably includes an anti-oxidant and a chelatingagent that inhibits the degradation of the compound. Preferredantioxidants for some compounds are BHT, BHA, alpha-tocopherol andascorbic acid in the preferred range of about 0.01% to 0.3% and morepreferably BHT in the range of 0.03% to 0.1% by weight by total weightof the composition. Preferably, the chelating agent is present in anamount of from 0.01% to 0.5% by weight by total weight of thecomposition. Particularly preferred chelating agents include edetatesalts (e.g. disodium edetate) and citric acid in the weight range ofabout 0.01% to 0.20% and more preferably in the range of 0.02% to 0.10%by weight by total weight of the composition. The chelating agent isuseful for chelating metal ions in the composition that may bedetrimental to the shelf life of the formulation. While BHT and disodiumedetate are the particularly preferred antioxidant and chelating agentrespectively for some compounds, other suitable and equivalentantioxidants and chelating agents may be substituted therefore as wouldbe known to those skilled in the art.

Liquid suspensions may be prepared using conventional methods to achievesuspension of the active ingredient in an aqueous or oily vehicle.Aqueous vehicles include, for example, water, and isotonic saline. Oilyvehicles include, for example, almond oil, oily esters, ethyl alcohol,vegetable oils such as arachis, olive, sesame, or coconut oil,fractionated vegetable oils, and mineral oils such as liquid paraffin.Liquid suspensions may further comprise one or more additionalingredients including, but not limited to, suspending agents, dispersingor wetting agents, emulsifying agents, demulcents, preservatives,buffers, salts, flavorings, coloring agents, and sweetening agents. Oilysuspensions may further comprise a thickening agent. Known suspendingagents include, but are not limited to, sorbitol syrup, hydrogenatededible fats, sodium alginate, polyvinylpyrrolidone, gum tragacanth, gumacacia, and cellulose derivatives such as sodium carboxymethylcellulose,methylcellulose, hydroxypropylmethylcellulose. Known dispersing orwetting agents include, but are not limited to, naturally-occurringphosphatides such as lecithin, condensation products of an alkyleneoxide with a fatty acid, with a long chain aliphatic alcohol, with apartial ester derived from a fatty acid and a hexitol, or with a partialester derived from a fatty acid and a hexitol anhydride (e.g.,polyoxyethylene stearate, heptadecaethyleneoxycetanol, polyoxyethylenesorbitol monooleate, and polyoxyethylene sorbitan monooleate,respectively). Known emulsifying agents include, but are not limited to,lecithin, and acacia. Known preservatives include, but are not limitedto, methyl, ethyl, or n-propyl-para-hydroxybenzoates, ascorbic acid, andsorbic acid. Known sweetening agents include, for example, glycerol,propylene glycol, sorbitol, sucrose, and saccharin. Known thickeningagents for oily suspensions include, for example, beeswax, hardparaffin, and cetyl alcohol.

Liquid solutions of the active ingredient in aqueous or oily solventsmay be prepared in substantially the same manner as liquid suspensions,the primary difference being that the active ingredient is dissolved,rather than suspended in the solvent. As used herein, an “oily” liquidis one which comprises a carbon-containing liquid molecule and whichexhibits a less polar character than water. Liquid solutions of thepharmaceutical composition of the invention may comprise each of thecomponents described with regard to liquid suspensions, it beingunderstood that suspending agents will not necessarily aid dissolutionof the active ingredient in the solvent. Aqueous solvents include, forexample, water, and isotonic saline. Oily solvents include, for example,almond oil, oily esters, ethyl alcohol, vegetable oils such as arachis,olive, sesame, or coconut oil, fractionated vegetable oils, and mineraloils such as liquid paraffin.

Powdered and granular formulations of a pharmaceutical preparation ofthe invention may be prepared using known methods. Such formulations maybe administered directly to a subject, used, for example, to formtablets, to fill capsules, or to prepare an aqueous or oily suspensionor solution by addition of an aqueous or oily vehicle thereto. Each ofthese formulations may further comprise one or more of dispersing orwetting agent, a suspending agent, and a preservative. Additionalexcipients, such as fillers and sweetening, flavoring, or coloringagents, may also be included in these formulations.

A pharmaceutical composition of the invention may also be prepared,packaged, or sold in the form of oil-in-water emulsion or a water-in-oilemulsion. The oily phase may be a vegetable oil such as olive or arachisoil, a mineral oil such as liquid paraffin, or a combination of these.Such compositions may further comprise one or more emulsifying agentssuch as naturally occurring gums such as gum acacia or gum tragacanth,naturally-occurring phosphatides such as soybean or lecithinphosphatide, esters or partial esters derived from combinations of fattyacids and hexitol anhydrides such as sorbitan monooleate, andcondensation products of such partial esters with ethylene oxide such aspolyoxyethylene sorbitan monooleate. These emulsions may also containadditional ingredients including, for example, sweetening or flavoringagents.

Methods for impregnating or coating a material with a chemicalcomposition are known in the art, and include, but are not limited tomethods of depositing or binding a chemical composition onto a surface,methods of incorporating a chemical composition into the structure of amaterial during the synthesis of the material (i.e., such as with aphysiologically degradable material), and methods of absorbing anaqueous or oily solution or suspension into an absorbent material, withor without subsequent drying.

The regimen of administration may affect what constitutes an effectiveamount. The therapeutic formulations may be administered to the subjecteither prior to or after a diagnosis of disease. Further, severaldivided dosages, as well as staggered dosages may be administered dailyor sequentially, or the dose may be continuously infused, or may be abolus injection. Further, the dosages of the therapeutic formulationsmay be proportionally increased or decreased as indicated by theexigencies of the therapeutic or prophylactic situation.

Administration of the compositions of the present invention to asubject, preferably a mammal, more preferably a human, may be carriedout using known procedures, at dosages and for periods of time effectiveto prevent or treat disease. An effective amount of the therapeuticcompound necessary to achieve a therapeutic effect may vary according tofactors such as the activity of the particular compound employed; thetime of administration; the rate of excretion of the compound; theduration of the treatment; other drugs, compounds or materials used incombination with the compound; the state of the disease or disorder,age, sex, weight, condition, general health and prior medical history ofthe subject being treated, and like factors well-known in the medicalarts. Dosage regimens may be adjusted to provide the optimum therapeuticresponse. For example, several divided doses may be administered dailyor the dose may be proportionally reduced as indicated by the exigenciesof the therapeutic situation. A non-limiting example of an effectivedose range for a therapeutic compound of the invention is from about 1and 5,000 mg/kg of body weight/per day. One of ordinary skill in the artwould be able to study the relevant factors and make the determinationregarding the effective amount of the therapeutic compound without undueexperimentation.

The compound may be administered to a subject as frequently as severaltimes daily, or it may be administered less frequently, such as once aday, once a week, once every two weeks, once a month, or even lessfrequently, such as once every several months or even once a year orless. It is understood that the amount of compound dosed per day may beadministered, in non-limiting examples, every day, every other day,every 2 days, every 3 days, every 4 days, or every 5 days. For example,with every other day administration, a 5 mg per day dose may beinitiated on Monday with a first subsequent 5 mg per day doseadministered on Wednesday, a second subsequent 5 mg per day doseadministered on Friday, and so on. The frequency of the dose will bereadily apparent to the skilled artisan and will depend upon any numberof factors, such as, but not limited to, the type and severity of thedisease being treated, the type and age of the animal, etc.

Actual dosage levels of the active ingredients in the pharmaceuticalcompositions of this invention may be varied so as to obtain an amountof the active ingredient that is effective to achieve the desiredtherapeutic response for a particular subject, composition, and mode ofadministration, without being toxic to the subject.

A medical doctor, e.g., physician or veterinarian, having ordinary skillin the art may readily determine and prescribe the effective amount ofthe pharmaceutical composition required. For example, the physician orveterinarian could start doses of the compounds of the inventionemployed in the pharmaceutical composition at levels lower than thatrequired in order to achieve the desired therapeutic effect andgradually increase the dosage until the desired effect is achieved.

In particular embodiments, it is especially advantageous to formulatethe compound in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the subjects tobe treated; each unit containing a predetermined quantity of therapeuticcompound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical vehicle. The dosage unitforms of the invention are dictated by and directly dependent on (a) theunique characteristics of the therapeutic compound and the particulartherapeutic effect to be achieved, and (b) the limitations inherent inthe art of compounding/formulating such a therapeutic compound for thetreatment of a disease in a subject.

In one embodiment, the compositions of the invention are administered tothe subject in dosages that range from one to five times per day ormore. In another embodiment, the compositions of the invention areadministered to the subject in range of dosages that include, but arenot limited to, once every day, every two, days, every three days toonce a week, and once every two weeks. It will be readily apparent toone skilled in the art that the frequency of administration of thevarious combination compositions of the invention will vary from subjectto subject depending on many factors including, but not limited to, age,disease or disorder to be treated, gender, overall health, and otherfactors. Thus, the invention should not be construed to be limited toany particular dosage regime and the precise dosage and composition tobe administered to any subject will be determined by the attendingphysical taking all other factors about the subject into account.

Compounds of the invention for administration may be in the range offrom about 1 mg to about 10,000 mg, about 20 mg to about 9,500 mg, about40 mg to about 9,000 mg, about 75 mg to about 8,500 mg, about 150 mg toabout 7,500 mg, about 200 mg to about 7,000 mg, about 3050 mg to about6,000 mg, about 500 mg to about 5,000 mg, about 750 mg to about 4,000mg, about 1 mg to about 3,000 mg, about 10 mg to about 2,500 mg, about20 mg to about 2,000 mg, about 25 mg to about 1,500 mg, about 50 mg toabout 1,000 mg, about 75 mg to about 900 mg, about 100 mg to about 800mg, about 250 mg to about 750 mg, about 300 mg to about 600 mg, about400 mg to about 500 mg, and any and all whole or partial incrementstherebetween.

In some embodiments, the dose of a compound of the invention is fromabout 1 mg and about 2,500 mg. In some embodiments, a dose of a compoundof the invention used in compositions described herein is less thanabout 10,000 mg, or less than about 8,000 mg, or less than about 6,000mg, or less than about 5,000 mg, or less than about 3,000 mg, or lessthan about 2,000 mg, or less than about 1,000 mg, or less than about 500mg, or less than about 200 mg, or less than about 50 mg. Similarly, insome embodiments, a dose of a second compound (i.e., a drug used fortreating the same or another disease as that treated by the compositionsof the invention) as described herein is less than about 1,000 mg, orless than about 800 mg, or less than about 600 mg, or less than about500 mg, or less than about 400 mg, or less than about 300 mg, or lessthan about 200 mg, or less than about 100 mg, or less than about 50 mg,or less than about 40 mg, or less than about 30 mg, or less than about25 mg, or less than about 20 mg, or less than about 15 mg, or less thanabout 10 mg, or less than about 5 mg, or less than about 2 mg, or lessthan about 1 mg, or less than about 0.5 mg, and any and all whole orpartial increments thereof.

In one embodiment, the present invention is directed to a packagedpharmaceutical composition comprising a container holding atherapeutically effective amount of a compound or conjugate of theinvention, alone or in combination with a second pharmaceutical agent;and instructions for using the compound or conjugate to treat, prevent,or reduce one or more symptoms of a disease in a subject.

The term “container” includes any receptacle for holding thepharmaceutical composition. For example, in one embodiment, thecontainer is the packaging that contains the pharmaceutical composition.In other embodiments, the container is not the packaging that containsthe pharmaceutical composition, i.e., the container is a receptacle,such as a box or vial that contains the packaged pharmaceuticalcomposition or unpackaged pharmaceutical composition and theinstructions for use of the pharmaceutical composition. Moreover,packaging techniques are well known in the art. It should be understoodthat the instructions for use of the pharmaceutical composition may becontained on the packaging containing the pharmaceutical composition,and as such the instructions form an increased functional relationshipto the packaged product. However, it should be understood that theinstructions may contain information pertaining to the compound'sability to perform its intended function, e.g., treating or preventing adisease in a subject, or delivering an imaging or diagnostic agent to asubject.

Routes of administration of any of the compositions of the inventioninclude oral, nasal, rectal, parenteral, sublingual, transdermal,transmucosal (e.g., sublingual, lingual, (trans)buccal, (trans)urethral,vaginal (e.g., trans- and perivaginally), (intra)nasal, and(trans)rectal), intravesical, intrapulmonary, intracerebral, epidural,intracerebroventricular, intraduodenal, intragastrical, intrathecal,subcutaneous, intramuscular, intradermal, intra-arterial, intravenous,intrabronchial, inhalation, and topical administration.

Suitable compositions and dosage forms include, for example, tablets,capsules, caplets, pills, gel caps, troches, dispersions, suspensions,solutions, syrups, granules, beads, transdermal patches, gels, powders,pellets, magmas, lozenges, creams, pastes, plasters, lotions, discs,suppositories, liquid sprays for nasal or oral administration, drypowder or aerosolized formulations for inhalation, compositions andformulations for intravesical administration and the like. It should beunderstood that the formulations and compositions that would be usefulin the present invention are not limited to the particular formulationsand compositions that are described herein.

Diagnostic Methods

The present invention provides a method to diagnose a subject having orat risk for developing a disease or disorder associated with proteinmisfolding or protein aggregates. For example, in one embodiment, themethod comprises using the level of expression or activity of one ormore TRIM proteins or one or more STUbLs as diagnostic markers. In oneembodiment, the method comprises detecting the presence of a geneticmutation in a nucleic acid encoding one or more TRIM proteins or one ormore STUbLs.

In one embodiment, the method is used to diagnose a subject as having adisease or disorder associated with protein misfolding or proteinaggregates. In one embodiment, the method is used to diagnose a subjectas being at risk for developing a disease or disorder associated withprotein misfolding or protein aggregates. In one embodiment, the methodis used to evaluate the effectiveness of a therapy for aneurodegenerative disease or disorder associated with protein misfoldingor protein aggregates.

In one embodiment, the method comprises collecting a biological samplefrom a subject. Exemplary samples include, but are not limited to blood,urine, feces, sweat, bile, serum, plasma, tissue biopsy, and the like.For example, in one embodiment, the sample comprises at least one cellof neural tissue. In one embodiment, the sample comprises a neuron,astrocyte, oligodendrocyte, Perkinje cell, pyramidal cell, or the like.

Methods for detecting a reduced expression or activity of one or moreTRIM proteins or one or more STUbLs comprise any method thatinterrogates a gene or its products at either the nucleic acid orprotein level. Such methods are well known in the art and include, butare not limited to, nucleic acid hybridization techniques, nucleic acidreverse transcription methods, and nucleic acid amplification methods,western blots, northern blots, southern blots, ELISA,immunoprecipitation, immunofluorescence, flow cytometry,immunocytochemistry. In particular embodiments, disrupted genetranscription is detected on a protein level using, for example,antibodies that are directed against specific proteins. These antibodiescan be used in various methods such as Western blot, ELISA,immunoprecipitation, flow cytometry, or immunocytochemistry techniques.

Methods of Manufacturing Recombinant Protein

In certain embodiments, the present invention provides a method of usingone or more TRIM proteins, one or more STUbLs, or a combination thereof,in the production of a recombinant protein of interest. For example, theone or more TRIM proteins, one or more STUbLs, or a combination thereof,can be used to disaggregate protein aggregates of the recombinantprotein of interest, thereby allowing for the production and collectionof the recombinant protein of interest.

In certain embodiments, the method comprises administering to a cell oneor more TRIM proteins, one or more STUbLs, a nucleic acid moleculeencoding one or more TRIM proteins, a nucleic acid molecule encoding oneor more STUbLs, or a combination thereof. In certain embodiments, thecell is modified to express the recombinant protein of interest. Thecell may be of any expression system, including, but not limited to ayeast expression system, bacterial expression system, insect expressionsystem, or mammalian expression system.

EXPERIMENTAL EXAMPLES

The invention is further described in detail by reference to thefollowing experimental examples. These examples are provided forpurposes of illustration only, and are not intended to be limitingunless otherwise specified. Thus, the invention should in no way beconstrued as being limited to the following examples, but rather, shouldbe construed to encompass any and all variations which become evident asa result of the teaching provided herein.

Without further description, it is believed that one of ordinary skillin the art can, using the preceding description and the followingillustrative examples, make and utilize the present invention andpractice the claimed methods. The following working examples therefore,specifically point out the preferred embodiments of the presentinvention, and are not to be construed as limiting in any way theremainder of the disclosure.

Example 1: A Cellular System that Degrades Misfolded Proteins andProtects Against Neurodegeneration

Misfolded proteins compromise cellular function and cause disease. Howthese proteins are detected and degraded is not well understood. Theexperiments presented herein show that PML (also known as TRIM19) andthe SUMO-dependent ubiquitin ligase RNF4 act together to promote thedegradation of misfolded proteins in the mammalian cell nucleus. PMLselectively interacts with misfolded proteins through distinct substraterecognition sites and conjugates these proteins with the smallubiquitin-like modifiers (SUMOs) through its SUMO ligase activity.SUMOylated misfolded proteins are then recognized and ubiquitinated byRNF4 and are subsequently targeted for proteasomal degradation. Further,it is demonstrated herein that PML deficiency exacerbates polyglutamine(polyQ) disease in a mouse model of spinocerebellar ataxia 1 (SCA1).These findings reveal a mammalian system that removes misfolded proteinsthrough sequential SUMOylation and ubiquitination and define its role inprotection against protein-misfolding diseases.

The promyelocytic leukemia protein (PML; also known as TRIM19) is amember of the tripartite motif (TRIM) family of proteins, which containan N-terminal TRIM/BRCC region, consisting of a RING domain, one or twoB boxes, and a coiled-coil (CC) motif, followed by a variable C-terminalregion. PML is predominantly a nuclear protein and is the eponymouscomponent of PML nuclear bodies. It is implicated in a wide variety ofcell processes, including apoptosis, transcription, DNA damagesignaling, and antiviral responses (Bernardi and Pandolfi, 2007, Nat RevMol Cell Biol, 8: 1006-1016). Notably, PML also colocalizes withaggregates formed by polyQ proteins associated with SCAs (Skinner etal., 1997, Nature, 389, 971-974; Takahashi et al., 2003, Neurobiol Dis,13: 230-237) and, upon overexpression, promotes degradation of at leastone of them (mutant ataxin-7) (Janer et al., 2006, J Cell Biol, 174:65-76). Despite the potential importance of these observations, the roleof PML in the removal of misfolded proteins is not well understood. Inparticular, it is unclear whether PML plays a broad role in the removalof nuclear misfolded proteins. The critical issue of the molecularmechanisms by which PML removes misfolded proteins is unaddressed.Moreover, the physiological relevance of the effect of PML on misfoldedproteins is not known.

The materials and methods employed in these experiments are nowdescribed.

Plasmids

All proteins are of human origin unless otherwise indicated. Plasmidsfor expressing the following proteins in mammalian cells were made inpRK5 by PCR, and each was fused with HA, FLAG, or 6×His tag, or GST orGFP protein at the NH2- or COOH-terminus as indicated: FLAG-PML mutants(isoform IV unless otherwise indicated); GST-PML; Atxn1 82Q-GFP,HA-Atxn1 82Q-FLAG, FLAG-Atxn1 82Q; HA-Httex1p 97QP and HA-Httex1p97QP(KR); FLAG-nFluc-GFP, FLAG-nFlucSM-GFP, and FLAG-nFlucDM-GFP;HA-RNF4, HA-RNF4 SIMm, HA-RNF4-FLAG, and HA-RNF4 SIMm-FLAG; and HA-SUMO2KR. Atxn1 82Q plasmids were made based on the FLAG-Atxn1 82Q/pcDNAplasmid provided by H. Orr (Riley et al., 2005, J Biol Chem, 280:21942-21948); Httex1p 97QP and Httex1p 97QP(KR) (in which K6, K9, andK15 were changed to Arg) are based on Steffan et al., 2004, Science,304: 100-104; and nFluc plasmids based on Gupta et al., 2011, NatMethods, 8: 879-884. Each nFluc protein was fused to the SV40 nuclearlocalization signal (PKKKRKV) (SEQ ID NO: 147) at the NH2-terminus andto GFP at the COOH-terminus. In FlucDM, R188 and R261 were changed toGlu; In FlucSM, R188 was changed to Glu (Gupta et al., 2011, NatMethods, 8: 879-884). The template for PCR amplification of RNF4 waspurchased from Open Biosystems (gene accession number: NM002938). InRNF4 SIMm, the following resides within SIMs were changed to Ala: I36,L38, and V39 (SIM1); I46, V47, and L49 (SIM2); V57, V58, and V59 (SIM3);and V67, V68, I69 and V70 (SIM4). In SUMO2 KR, the internal SUMOylationconsensus site Lys11 was mutated to Arg.

For bacterial expression, GST fusions of Htt 25Q, Htt 103Q, Htt 52Q, Htt52Q cc-, PML CC-FLAG, RNF4, and RNF4 SIMm were constructed in pGEX-1ZT,a derivative of pGEX-1λT with additional cloning sites. Htt 25Q, Htt 52Qand Htt 103Q contained the Htt amino acids 1-17 followed by a polyQstretch of the indicated length (Krobitsch and Lindquist, 2000, ProcNatl Acad Sci USA, 97: 1589-1594). Htt 52Q and Htt 52Q cc-cDNAs wereassembled by joining synthetic oligos. FLAG-PML F12 (571-633)-6×His wasconstructed in pET28a. All plasmids generated for this study wereconfirmed by DNA sequencing.

The following plasmids were previously described: FLAG-PML, FLAG-PML M6(which had the C57S, C60S, C129A, C132A, C189A, and H194A mutations),6×His-SUMO1, and 6×His-SUMO2 (Chu and Yang, 2011, Oncogene, 30:1108-1116); FLAG-Atxn1 82Q and FLAGAtxn1 30Q (Riley et al., 2005, J BiolChem, 280: 21942-21948); luciferase-6×His (a Photinus pyralis luciferasevariant) (Sharma et al., 2010, Nat Chem Biol, 6: 914-920); GST-rRNF4(where “r” denotes rat origin, same below), GSTrRNF4 CS1 (in which C136and C139 were changed to Ser), FLAG-rRNF4, and FLAGrRNF4 CS (in whichC136, C139, C177, and C180 were changed to Ser) (Hakli et al., 2004,FEBS Lett, 560: 56-62); and PML isoforms I, II, III, IV, and VI (used inFIG. 8A) (Xu et al., 2005, Mol Cel, 17: 721-732).

siRNAs

PML and RNF4 siRNAs were purchased from Qiagen, and the sense strandsequences were: PML #4, CTCCAAGATCTAAACCGAGAA (SEQ ID NO: 148); PML #9,CACCCGCAAGACCAACAACAT (SEQ ID NO: 149); RNF4 #5, CCCTGTTTCCTAAGAACGAAA(SEQ ID NO: 150); RNF4 #6, TAGGCCGAGCTTTGCGGGAAA (SEQ ID NO: 151); RNF4#8, AAGACTGTTTCGAAACCAACA (SEQ ID NO: 152). RNF4 was knocked down witheither siRNAs individually or in combination at an equal molar ratio.SUMO1 siRNA (Thermo Scientific, siGENOME SMARTpool M-016005-03-0005) wasa pool of 4 target-specific siRNA duplexes. The sense strand sequenceswere: TCAAGAAACUCAAAGAATC (SEQ ID NO: 153), GACAGGGTGTTCCAATGAA (SEQ IDNO: 154), GGTTTCTCTTTGAGGGTCA (SEQ ID NO: 155), and GAATAAATGGGCATGCCAA(SEQ ID NO: 156). SUMO2/3 siRNAs (Santa Cruz sc-37167) was a pool ofthree different siRNA duplexes, and sense strand sequences were

(SEQ ID NO: 157) CCCAUUCCUUUAUUGUACA, (SEQ ID NO: 158)CAGAGAAUGACCACAUCAA, and (SEQ ID NO: 159) CAGUUAUGUUGUCGUGUAU

Cell Culture and Transfection

HeLa cells (from ATCC) and U2OS cells expressing GFP-SUMO2 or GFP-SUMO3(Mukhopadhyay et al., 2006, J Cell Biol, 174: 939-949) were maintainedin standard culture conditions. DNA plasmids were transfected into cellsusing Lipofectamine 2000. When PML and Atxn1 were co-transfected, eitherFLAG-PML plus Atxn1 82Q/30Q-GFP or HA-PML plus FLAG-Atxn1 82Q/30Q wasused. HA-RNF4 and HA-RNF4-FLAG plasmids were used for testing proteinexpression and cellular localization, respectively.

siRNAs using Lipofectamine 2000 or RNAiMAX (Invitrogen), according tothe manufacturer's instructions. For knockdown experiments, two roundsof siRNA transfection were performed on consecutive days. When both DNAand siRNA were transfected, DNA was transfected 4-6 hours aftertreatment with combined RNF4 siRNAs, and a day after treatment withother siRNAs. MG132 (Sigma) was added 24 hours after the lasttransfection at 7.5-10 μM (final concentration) for 4-5 hours.

Generation of RNF4 shRNA Stable Cell Lines

shRNA against human RNF4, cloned into pLKO.1, was obtained from ThermoScientific. The antisense sequence of shRNF4 is TGGCGTTTCTGGGAGTATGGG(SEQ ID NO: 160) (TRCN0000017054). For lentiviral production, 293T cellswere transfected with lentiviral vectors, Gag helper plasmid, Rev helperplasmid, and VSVG helper plasmid. Virus-containing media was collectedat 48 hours and 72 hours and spun for 5 minutes at 100 g. HeLa cellswere transduced using virus-containing supernatant with polybrene andselected with puromycin. The pLKO.1 vector was used to create controlstable cells.

Cell Lysate Fractionation, Filter Retardation Assay, and Western Blot

Cell lysates were made in NP-40-containing buffer and fractionated intosupernatant (NS) and pellet by centrifugation. Both fractions wereboiled in buffer containing 2% SDS and analyzed by western blot. Aportion of the pellet was analyzed by a filter retardation assay for SRspecies.

Samples were prepared as described with modifications (Janer et al.,2006, J Cell Biol, 174: 65-76). Cells were harvested and lysed for 30min on ice in buffer containing 50 mM Tris, pH 8.8, 100 mM NaCl, 5 mMMgCl₂, 0.5% NP-40, 2 mM DTT, 250 IU/ml benzonase (Sigma), 1 mM PMSF, 1×complete protease cocktail (Roche), and 20 mM N-Ethylmaleimide (NEM;Sigma). Protein concentrations were determined by Bradford assay(Bio-Rad Labs). The whole cell lysates were centrifuged at 13,000 rpmfor 15 minutes at 4° C. The supernatant, containing NP-40-soluble (NS)proteins, was analyzed by SDS-PAGE. The pellet was resuspended in thepellet buffer (20 mM Tris, pH 8.0, 15 mM MgCl₂, 2 mM DTT, 250 IU/mlbenzonase, 1 mM PMSF, 1×complete protease cocktail, and 20 mM NEM) andincubated for 30 minutes on ice. The pellet fraction was boiled in 2%SDS, 50 mM DTT. One portion of the boiled pellet fraction was resolvedby SDS-PAGE, and proteins entering the gel (SDS-soluble, SS) weredetected by Western blot. The other portion was applied to a membranefilter with 0.2 μm pore size as previously described (Wanker et al.,1999, Methods Enzymol, 309: 375-386), and the SDS-resistant (SR)aggregates retained on the filter was analyzed by immunoblotting.

Primary antibodies against the following proteins were used for Westernblot with product information and dilutions indicated: PML (rabbit,H-238, 1:1,000 and goat, N-19, 1:500), ubiquitin (mouse, P4D1,1:10,000), and HA (rabbit, Y-11, 1:500) (Santa Cruz Biotechnology); FLAG(mouse, M2, 1:7,500), actin (rabbit, 1:10,000), and p-tubulin (mouse,1:5,000) (Sigma); GFP (mouse, 1:4,000) (Clonetech); GST (goat, 1:1000,GE Healthcare Life Sciences); SUMO1 (mouse, 1:500, Invitrogen); SUMO2/3(rabbit, 1:250, Abgent); HA (for transfected HA-RNF4) (rat, 3F10,horseradish peroxidase or HRP-conjugated, 1:10,000) (Roche); RNF4(mouse, 1:500, Abnova, and a mouse monoclonal antibody developed byAbmart using antigen peptide DLTHNDSVVI (SEQ ID NO: 161), 1:1,000).Transfected FLAG-PML was detected by anti-FLAG antibody, and transfectedHA-PML and HA-RNF4 were detected by HA antibody.

The secondary antibodies were either conjugated to HRP (Santa CruzBiotechnology), or labeled with IRD Fluor 800 or IRD Fluor 680 (LI-COR,Inc.). Western blots were developed using ECL reagents and analyzedusing ImageJ, or scanned with the Odyssey infrared imaging system, andanalyzed using Image Studio Lite (LI-COR, Inc.).

Immunofluorescence of Cultured Cells

Cells cultured on coverslips were fixed with 4% paraformaldehyde for 15minutes, permeabilized with 0.2% Triton X-100 for 15 minutes, blockedwith 1% BSA, and incubated with antibodies as indicated. Cells weremounted with medium containing DAPI (for DNA detection) (Vector Labs),and the images were acquired with a Nikon Eclipse E800 or Olympus IX81microscope. The following primary antibodies were used with productinformation and concentrations indicated: PML (rabbit, H-238 and mouse,PG-M3, 1:100), RNF4 (goat, C-15, 1:25) (Santa Cruz Biotechnology), andFLAG (for transfected FLAG-PML and HA-RNF4-FLAG) (mouse, M2, 1:2,000)(Sigma). Secondary antibodies were FITC-conjugated anti-mouse,anti-rabbit (Zymed), and anti-goat (Invitrogen) IgGs; TexasRed-conjugated anti-mouse and anti-rabbit IgGs (Vector labs); andRhodamine Red-X conjugated anti-goat (Jackson ImmunoResearch Labs).

For quantification of Atxn1 82Q, Httex1p 97QP, and SUMO2-positive Atxn182Q aggregates, approximately 400, 500, and 200 cells, respectively,from ten or more randomly selected fields were examined. The sizes ofAtxn1 82Q inclusions were measured using ImageJ, and cells werecategorized based on the largest inclusion in cells. P-value for theproportions of cells with aggregates of various sizes in the presenceand the absence of PML was calculated using a chi-squared test. Forcells transfected with Httex1p 97QP, approximately 30% of them hadeither cytoplasmic or nuclear aggregates.

Assays of protein half-life

Cells were pulse labeled in Met- and Cys-free DMEM medium supplementedwith [³⁵S]Met and [³⁴S]Cys, and then cultured in regular DMEM.Alternatively, cells were treated with CHX. Immunoprecipitated[³⁵S]Atxn1 82Q or unlabeled Atxn1 82Q in cell lysate was analyzed byautoradiography or western blot.

For pulse-chase analysis, HeLa cells were transfected with FLAG-Atxn182Q alone or together with a moderate amount of PML. 17 h aftertransfection, cells were cultured in Met and Cys-free DMEM medium for 30min, and then pulse labeled for 30 min with [³⁵S]Met and [³⁵S]Cys (100μCi/ml each). Afterwards, cells were rinsed twice with PBS and chased inDMEM with 10% FBS for 0-18 h. Cells were lysed in IP-lysis buffer (50 mMHEPES, pH 7.5, 150 mM NaCl, 0.5% NP-40, and 2 mM DTT) containing 2% SDSand 50 mM DTT, and boiled at 95° C. for 10 minutes. The whole celllysates were centrifuged at 13,000 rpm for 15 minutes. The supernatantswere diluted 20-fold in IP-lysis buffer and incubated with anti-FLAG M2beads at 4° C. overnight. The beads were sequentially washed with IPlysis buffer with additional 0, 0.5 M, and 1 M KCl, and boiled in a 2%SDS sample buffer. Samples were resolved by SDS-PAGE and analyzed byautoradiography. To better compare the half-life of Atxn1 82Q underdifferent conditions, exposures with similar signal intensity at 0 hourswere presented.

For cycloheximide (CHX) treatment of Atxn1 82Q-transfected cells, 150g/ml CHX was added to cell culture medium 4-5 hours after transfection.Cells were harvested and snap-frozen on dry ice at indicated timepoints, lysed, and fractioned for Western blot analysis. For CHXtreatment of nFlucDM-transfected cells, 50 μg/ml CHX was added to cellculture medium 17 hours after transfection. Cells were harvested atindicated time points, and whole cell lysates were used for Western blotanalysis.

Quantitative RT-PCR Analysis

Total RNA was extracted using TRIzol (Invitrogen). cDNA synthesis wascarried out by reverse transcription of total RNA using the First StrandcDNA Synthesis Kit (Marligen Biosciences). A Tagman Gene ExpressionAssay (Applied Biosystems) with human Atxn1 (Hs00165656_m1) and 18s rRNA(4333760F) primers/probe sets were used for qPCR analysis.

Protein Purification

FLAG-PML, FLAG-PML M6, and FLAG-Atxn1 82Q-HA were expressed in 293Tcells and purified by anti-FLAG M2 beads (Sigma) as previously described(Tang et al., 2006, Nat Cell Biol, 8: 855-862; Tang et al., 2004, J BiolChem, 279: 20369-20377) with modifications. Cells were lysed in IP-lysisbuffer (50 mM Tris, pH 7.5, 150 mM NaCl, 0.5% Triton X-100, 0.5% NP-40and 2 mM DTT) supplemented with 1 mM PMSF, and 1×complete proteasecocktail. For PML purification, IP-lysis buffer was also supplementedwith 20 μM ZnCl2. The lysates were centrifuged at 13,000 rpm for 15minutes. Supernatants were incubated with anti-FLAG M2 beads at 4° C.for 4 hours to overnight. M2 beads were sequentially washed with IPlysis buffers containing 0, 0.5, and 1 M KCl, and with an elution buffer(50 mM Tris, pH 7.5, 150 mM NaCl, and 2 mM DTT). The bound proteins wereeluted in the elution buffer containing 0.1-0.3 mg/ml 3×FLAG peptide(Sigma). The major additional bands observed in the FLAG-PML andFLAG-PML M6 preps were derived from PML based on both Western blot andmass spectrometry analyses (FIG. 11G).

GST fusion of PML was expressed in 293T cells and purified usingglutathione-Sepharose™ 4B beads (GE Healthcare Life Sciences) withsimilar lysis and wash conditions as described above. GST fusions ofrRNF4, rRNF4 CS1, RNF4, and RNF4 SIMm were expressed in Escherichia coliBL21 DE3 or Rosetta 2 (EMD Chemicals) and purified as previouslydescribed (Hakli et al., 2001, J Biol Chem, 276: 23653-23660). Thebacteria were grown at 37° C. to A 600 nm=0.6-0.8, and were induced forprotein expression with 0.3 mM IPTG for 3 hours at 30° C. GST-taggedproteins were purified with glutathione beads. GST and GST fusions ofHtt 25Q, Htt 103Q were purified similarly except that 0.1 mM IPTG wasused for inducing protein expression. The bound proteins were eluted inthe elution buffer containing 30 mM glutathione (Sigma).

Luciferase-6×His was expressed in BL21 DE3 as previously described(Sharma et al., 2010, Nat Chem Biol, 6: 914-920). To generateimmobilized native luciferase, Luc (N), Ni-NTA beads (Qiagen) wereincubated with bacterial lysates and washed according to themanufacturer's instructions. Denatured luciferase, Luc (D), wasgenerated by treating immobilized Luc (N) with 8 M urea for 5 minutes. Aluciferase activity assay showed that only 0.2% of enzymatic activityremained after urea treatment. For control beads, lysates from bacteriaexpressing no luciferase were incubated with Ni-NTA beads in parallel.

To generate PML mutants used for luciferase peptide scans, FLAG-PML F12(571-633)-6×His and GST-PML CC-FLAG were expressed in BL21 DE cells atroom temperature with 0.1 mM IPTG induction for 3 hours and 1 hour,respectively. Flag-PML F12 (571-633)-6×His was purified first using M2beads and the FLAG peptide elution, and was subjected to a secondpurification using Ni-NTA beads, according to the manufacturer'sinstructions. To generate the PML CC domain, a TEV protease cleavagesite was introduced between GST and PML CC. The GST-PML CC-FLAGconjugated glutathione beads were incubated with TEV protease (Sigma)according to the manufacturer's instructions to release PML CC-FLAG fromthe GST moiety (and from the beads). PML CC-FLAG used for pull-downassay was generated by incubating the purified PML CC-FLAG proteins withM2 beads and washed as described above.

Pull-Down Assays

For FLAG pull-down assays, FLAG-PML, FLAG-GFP and PML CC-FLAG bound toanti-FLAG M2 beads were prepared as described above. Purified GST-Htt25Q, GST-Htt 103Q, GST-Htt 52Q or GST-Htt 52Q cc- were centrifuged at13,000 rpm for 15 minutes to remove any aggregated proteins. FLAG-PML(2.5 μg) or FLAG-GFP (1.1 μg) at comparable molarity was incubated withGST-Htt 25Q or GST-Htt 103Q (2.5 μg each) in the absence or presence ofHsp70 (2.5 μg) and Hsp40 (1.4 μg) (Enzo Life Sciences) in a final volumeof 200 μl assay buffer (50 mM Tris, pH 7.5, 150 mM NaCl, and 2 mM DTT,0.5% NP-40) for 2 hours at 4° C. The beads were washed three times withIP-lysis buffer in Compact Reaction Columns (Affymetrix/USB) and boiledin 2% SDS sample buffer. Samples were analyzed by Western blot. The PMLCC pull-down assay was performed similarly, except M2 beads containing1.6 μg PML CC-FLAG or control M2 beads were incubated with 5 μg GST orGST-Htt proteins.

For GST pull-down assay, 2 μg each of GST, GST-Htt 25Q, and GST-Htt 103Qproteins that bound to glutathione-Sepharose™ 4B beads were incubatedwith 400 g lysates from 293T cells expressing FLAG-PML protein at 4° C.for 4 hours. The beads were washed three times with IP-lysis buffer inCompact Reaction Columns and boiled in 2% SDS sample buffer. Sampleswere analyzed by Western blot. For detecting the interaction between PMLmutants and Htt, [³⁵S]Met-labeled full-length and mutant PML proteinswere generated using the SP6 Coupled Transcription/Translation System(Promega) and incubated with GST, GST-25Q and GST-Htt 103Q that bound tobeads in 150 μl IP-lysis buffer at 4° C. overnight. Beads were washedand boiled as described above. Input and pull-down samples were analyzedby autoradiography and Coomassie blue staining. For autoradiography,pull-down samples from the same experiments that were resolved ondifferent gels were subjected to the same exposure time.

For the luciferase pull-down assay, 3 μg of Luc (N) or Luc (D) boundNi-NTA beads or control beads prepared from an equal amount of bacteriallysate were incubated with purified GST (1 μg), GST-PML (3 μg) in theabsence or presence of Hsp70 (3 μg) and Hsp40 (1.7 μg), or[³⁵S]Met-labeled full-length and mutant PML proteins in 200 μl PBScontaining 15 mM Imidazole, 1 mM DTT, 0.5% Triton X-100 and 0.5% NP-40at 4° C. for 4 hours. The beads were washed three times with PBScontaining 20 mM Imidazole, 1 mM DTT, 0.5% Triton X-100 and 0.5% NP-40and boiled. The input and pull-down samples were analyzed as describedabove.

Screening of Cellulose-Bound Peptides for Binding to PML Domains

A peptide library (13-mers overlapping by ten amino acids) for Photinuspyralis luciferase was prepared by automated spot synthesis (JPT peptideTechnologies). The peptide array membrane was probed with purified PMLSRS1 and SRS2 fragments. The peptide array membrane was blocked withOdyssey Blocking buffer (LI-COR, Inc) and incubated with FLAG-PMLF12(571-633)-His×6 or PML F4/CC-FLAG (150 nM each) in TBS-T (50 mM TRIS,pH 8.0, 137 mM NaCl, 2.7 mM KCl, 0.05% Tween and 1 mM DTT) at 4° C. for2 hours. The membrane was washed and blotted with mouse anti-Flag andanti-mouse-HRP antibodies following the manufacturer's instructions. Theblots were developed using ECL reagents. Background signal on blots withanti-Flag and anti-mouse-HRP antibodies alone was minimal even at longexposures. The peptide array membrane was regenerated according to themanufacturer's protocol.

SUMOylation and Ubiquitination Analysis

Cells or in vitro reaction mixtures were boiled in buffer containing 2%SDS and then diluted in buffer without SDS or passed through a Bio-Spinchromatography column to reduce the SDS concentration. Proteins wereimmunoprecipitated (denaturing IP or d-IP) and analyzed by western blot.

In Vivo SUMOylation and Ubiquitination Assays

Cells were transfected with FLAG-Atxn1, FLAG-nFluc-GFP, and otherexpression plasmids as indicated. For the experiments shown in FIG. 4A,a SUMO2-expressing plasmid was also used. Twenty four hours aftertransfection, cells were treated with 7.5 μM MG132 or DMSO for 5 hoursor left untreated, and harvested in IP-lysis buffer supplemented with 2%SDS and 50 mM DTT. For denaturing immunoprecipitation (d-IP), celllysates were boiled at 95° C. for 10 minutes. One aliquot was saved forWestern blot analysis. The rest of the lysates were either diluted20-fold in IP-lysis buffer or passed through a Bio-Spin chromatographycolumn (Bio-Rad) equilibrated with IP-lysis buffer to reduce the SDSconcentration. Lysates were then incubated with anti-FLAG (M2) beads at4° C. for 4 hours or overnight. The beads were washed as described forFLAG-tagged protein purification, and boiled in 2% SDS sample buffer.Proteins from beads were analyzed by Western blot with anti-FLAG,-SUMO2/3, -SUMO1, -ubiquitin, and other antibodies as indicated. Tobetter compare the levels of ubiquitinated or SUMOylated species, d-IPproducts containing similar levels of unmodified proteins were oftenused for Western blot analysis.

In Vitro SUMOylation Assays

Components for in vitro ubiquitination and SUMOylation reactions werepurchased from Boston Biochem. In vitro SUMOylation assays wereperformed at 37° C. for 1.5 hours in 30 μl reaction buffer (50 mM TrispH 7.5, 5.0 mM Mg2+-ATP, and 2.5 mM DTT) containing purified HA-Atxn182Q-FLAG (600 ng/200 nM), FLAG-PML (for FIG. 4D, 50 and 200 ng or 22 and90 nM; for FIG. 4E 100 ng or 45 nM) or FLAG-PML M6 (100 ng or 45 nM),SAE1/SAE2 (125 nM), Ubc9 (1 μM), His-SUMO2 (25 μM), Hsp70 (420 ng/200nM), Hsp40 (240 ng/200 nM) and BSA (0.1 μg/ml). The reaction mixtureswere denatured by the addition of 30 μl IP-lysis buffer containing 2%SDS and 50 mM DTT and heating at 95° C. for 10 minutes. One aliquot ofthe heated reaction mixes were saved for Western blot analysis, and therest were diluted 20-fold in IP-lysis buffer without SDS. HA-Atxn1-FLAGwas immunoprecipitated by anti-HA beads (Roche) and analyzed for SUMO2/3modification using anti-SUMO2/3 antibodies.

In Vitro Ubiquitination Assays

In vitro assays for RNF4 self-ubiquitination were performed at 37° C.for 1 hour in 10 μl reaction buffer (50 mM Tris pH 7.5 and 2.5 mM DTT)containing purified GST-RNF4 protein (250 ng/530 nM), UBE1 (125 nM),UbcH5a (625 nM), ubiquitin (2.5 g/30 μM), and Mg²⁺-ATP (2.5 mM). Thereaction mixtures were heated at 95° C. for 10 minutes and analyzed byWestern blot.

For in vitro ubiquitination of SUMOylated Atxn1 82Q, a mix of SUMOylatedand unmodified Atxn1 82Q proteins was prepared as ubiquitinationreaction substrate. M2 beads conjugated with FLAG-Atxn1 82Q-HA (1.5μg/300 nM) and control M2 beads were mixed with 0.75 μM SAE1/SAE2, 12.5μM Ubc9, 125 μM His-SUMO2, and 2.5 mM DTT in a total volume of 50 μl ofMg2+-ATP-Energy Regeneration Solution containing 5 mM ATP (BostonBiochem). To achieve sufficient Atxn1 82Q SUMOylation, the reaction wasperformed at 37° C. for 24 hours, and the reaction buffer was replacedafter 12 hours. Beads were then washed sequentially with IP-lysis bufferwith additional 0, 0.5, and 1 M KCl and with ubiquitination reactionbuffer (50 mM Tris pH 7.5 and 150 mM NaCl) (Tang et al., 2006, Nat CellBiol, 8: 855-862).

Atxn1 82Q beads and control beads were then incubated at 37° C. for 1hour with ubiquitination reaction mixes in 20 μl volume containingGST-rRNF4 (0, 40, 160 and 500 ng, or 0, 43, 170, and 530 nM), UBE1 (100nM), UbcH5a (500 nM), ubiquitin (5 μg/30 μM), and Mg²⁺-ATP (2.5 mM) inreaction buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, and 2.5 mM DTT).Afterwards, beads were separated from the supernatant and washed withIP-lysis buffer. Atxn1 82Q was denatured and released from the beads bythe addition of IP-lysis buffer containing 2% SDS and 50 mM DTT and heatat 95° C. for 10 minutes. After dilution, Atxn1 82Q wasimmunoprecipitated with M2 beads. The IP products and the supernatantfrom the reaction were analyzed by Western blot.

Mouse Breeding and Genotyping

The heterozygous B05 transgenic mice (Atxn1^(tg/−)), which harbor thehuman SCA1-coding region with 82 CAG repeats driven by a Purkinjecell-specific promoter element, were provided (Burright et al., 1995,Cell, 82: 937-948). PML^(−/−) mice were provided (Wang et al., 1998,Science, 279: 1547-1551). Atxn1^(tg/−) mice (on FVB background) weremated with PML^(−/−) (on 129Sv background). PML^(+/−):Atxn1^(tg/−) icefrom the F1 generation were mated with PML^(−/−) or PML^(+/+) togenerate mice used for Rotarod tests and pathology. The mating schemedid not affect the Rotarod performance, formation of aggregates,molecular layer thickness, or dendritic arborization of the F2generation of PML+ or PML^(+/−):Atxn1^(tg/−) mice. The mouse genotypewas determined by PCR either as described (Burright et al., 1995, Cell,82: 937-948) (for Atxn1) or according to suggestions by the NCI MouseRepository (for PML).

Accelerating Rotarod Test

An accelerating Rotarod apparatus (47600, Ugo Basile, Italy) was used tomeasure motor coordination and balance. Only naïve animals were used.Each animal was given three trials per day for four consecutive days,with a 1 hour rest between trials. For each trial, mice was placed onthe Rotarod with increasing speed, from 4-80 rpm, over 10 minutes. Theirlatency to fall off the Rotarod (in seconds) was recorded.

Immunostaining and Pathological Analysis of Mouse Cerebellum

Paraffin-embedded cerebellar midsagital sections were stained withindicated antibodies and visualized using a Leica SP5 II laser scanningconfocal microscope, or stained with hematoxylin and visualized using anOlympus BX51 microscope.

Immunohistochemistry and immunofluorescence were performed as previouslydescribed with modifications (Duda et al., 2000, J Neuropathol ExpNeurol, 59: 830-841; Emmer et al., 2011, J Biol Chem 286: 35104-35118).Paraffin-embedded cerebella were cut into 10-μm sections. For molecularlayer measurements, three haematoxylin stained midsagittal sections with100 μm intervals were analyzed per mouse. Twenty measurements at theprimary fissure for each section were averaged.

To quantify Purkinje cell dendritic arborization, midsagittal sectionsof cerebella were stained with an antibody against the Purkinjecell-specific protein calbindin (mouse, CB-955, 1:250; Sigma). Twenty0.5 μm optical sections were accumulated with Leica SP5 II laserscanning confocal microscope. The brightest continuous 12 sections (6μm) were projected for maximum intensity. The fluorescence intensityprofile from the same region of preculminate fissure was plotted usingImageJ.

To quantify Purkinje cells, midsagittal sections were stained withanti-calbindin antibody and comparable regions were used for cellcounting. The length of the Purkinje cell layer was measured by drawingsegmented line along Purkinje cell soma center using ImageJ. For eachmouse, 350-900 neurons along approximately 30 mm were measured. ThePurkinje cell density was determined by dividing the number of cells bythe length of Purkinje cell layer.

To determine the number of Purkinje cells with aggregates, midsagittalsections were stained with anti-ubiquitin (mouse, Ubi-1, MAB1510,1:2,000; Millipore) antibody. Three hundred cells or more were countedfrom the same brain regions per mouse. Images were taken using anOlympus BX51 microscope mounted with a DP71 Olympus digital camera.

Four mice per genotype were used for counting Purkinje cells of1-year-old mice, two PML^(+/−) mice per genotype for quantification ofdendritic arborization, and three mice per genotype for the rest of thestudies.

Statistical Analysis

The numbers of cells with aggregates were analyzed by chi-squared testand Student's t-test when appropriate. The behavioral scores andcerebellar pathology were analyzed by two-way ANOVA with repeatedmeasurements and Student's t-test. All the data were analyzed usingPrism5 software or Microsoft Excel 2008.

The results of the experiments are now described

PML Promotes Proteasomal Degradation of Pathogenic Ataxin-1 Protein

SCA1 is a fatal neurological disorder characterized by progressiveataxia and loss of neurons, especially cerebellar Purkinje cells. It iscaused by the expansion of a polyQ stretch in the SCA1 gene product,Ataxin-1 (Atxn1) (Orr and Zoghbi, 2007, Annu Rev Neurosci, 30: 575-621).To investigate the role of PML in eliminating nuclear misfoldedproteins, a cell culture model was generated in which a pathogenic Atxn1protein with 82 contiguous glutamines that was C-terminally fused to theenhanced green fluorescent protein, Atxn1 82Q-GFP, was expressed in HeLacells. Similar to pathogenic Atxn1 proteins in human SCA1 patients andmouse SCA1 transgenic models (Skinner et al., 1997, Nature, 389:971-974), Atxn1 82Q-GFP was localized to the nucleus, exhibiting adiffuse localization pattern with markedly higher concentration inmicroscopically visible inclusions (FIG. 1A and FIG. 1 ). Atxn1 82Q-GFPalso yielded both NP-40-soluble (soluble or NS) and NP-40-insoluble(aggregated) species in cell lysates. The latter could be furtherdivided into SDS-soluble (SS) and SDS-resistant (SR) species (FIG. 1C).

Concordant with previous reports (Skinner et al., 1997, Nature, 389:971-974), endogenous PML colocalized with Atxn1 82Q-GFP inclusions,accumulating in bodies adjacent to them and also being distributedwithin (FIG. 1A). PML is expressed as several isoforms (Nisole et al.,2013, Front Oncol, 3: 125). Five major PML isoforms (I, II, III, IV, andVI) were examined and it was found that all five colocalized withAtxn1-GFP inclusions (FIG. 8A). For subsequent analyses, the commonlyused isoform IV (hereafter called PML unless otherwise noted) waschosen.

When co-expressed with Atxn1 82Q, PML significantly decreased the sizeof Atxn1 82Q-GFP nuclear inclusions (FIG. 1 ). It also reduced thesteady-state levels of the Atxn1 82Q-GFP protein, especially theaggregated SS and SR species (FIG. 1C, left). To evaluate the effect ofendogenous PML (all isoforms), it was knocked down using two independentsmall interfering RNAs (siRNAs). This noticeably raised the levels ofAtxn1 82Q-GFP, especially aggregated species (FIG. 1C, right). SilencingPML also increased the steady-state levels of a FLAG-tagged Atxn1 82Qprotein (FIG. 8B). The effect of PML siRNA on Atxn1 82Q could bereversed by an siRNA-resistant form of PML (FIG. 8C), ruling outoff-target effects of the siRNA.

To evaluate whether PML specifically reduces pathogenic Atxn1 proteins,a nonpathogenic ataxin-1 protein, Atxn1 30Q, was used. Forced expressionof PML did not reduce the abundance of Atxn1 30Q-GFP, while knockdown ofPML did not significantly augment it either (FIG. 1D), underscoring theselective effect of PML on pathogenic Atxn1 proteins.

PML did not inhibit the transcription of the Atxn1 82Q gene (FIG. 8D).To determine whether PML promotes the degradation of the Atxn1 82Qprotein, a pulse-chase assay was performed. In the absence ofco-transfected PML, total [³⁵S]-labeled Atxn1 82Q protein was ratherstable, and its levels declined only ˜20% in 18 hours. By contrast, inthe presence of PML, total [³⁵S]Atxn1 82Q protein was destabilized, andits levels declined ˜80% over the same period of time (FIG. 1E).

Experiments were conducted using cycloheximide (CHX) to block proteinsynthesis and to investigate the degradation of the pre-existing Atxn182Q protein. Forced expression of PML accelerated the degradation ofaggregated Atxn1 82Q, reducing its half-life from ˜8 hours to ˜2 hours,while having a minimal effect on soluble Atxn1 82Q (FIG. 1F).Conversely, silencing PML prolonged the half-life of aggregated Atxn182Q and, to a lesser extent, the half-life of soluble Atxn1 82Q (FIG.1G). The ability of PML to remove aggregated Atxn1 82Q was markedlydiminished by the proteasome inhibitor MG132 (FIG. 1H). In contrast, PMLdid not alter the half-life of Atxn1 30Q (FIG. 8E). Collectively, theseresults indicate that PML targets pathogenic, but not normal, Atxn1protein for proteasomal degradation.

A General Role for PML in Degrading Nuclear Misfolded Proteins

To assess whether PML plays a broad role in degrading misfolded proteinsin the nucleus, two additional proteins linked to neurodegeneration weretested: (1) a pathogenic fragment of huntingtin (Htt) encoded by thefirst exon of the HD gene, Httex1p 97QP (Steffan et al., 2004, Science,304: 100-104); and (2) TAR DNA-binding protein 43 (TDP-43), which isassociated with both amyotrophic lateral sclerosis (ALS, also known asLou Gehrig's disease) and frontotemporal lobar degeneration withubiquitinated inclusions (FTLD-U) (Chen-Plotkin et al., 2010, Nat RevNeurosci, 6: 211-220). Httex1p 97QP formed microscopically visibleinclusions in both the nucleus and the cytoplasm (FIG. 1I), while TDP-43formed inclusions mainly in the nucleus. PML reduced the nuclear, butnot the cytoplasmic, Httex1p 97QP inclusions (FIG. 1I), and decreasedthe amount of aggregated Httex1p 97QP (FIG. 1J, lanes 1 and 2). PML alsolowered the amount of aggregated, but not soluble, TDP-43 (FIG. 1K).

To extend these analyses, a structurally destabilized mutant of themodel chaperone substrate firefly luciferase (FlucDM) was used, whichwas developed as a probe for the capacity of cellular PQC systems (Guptaet al., 2011, Nat Methods, 8: 879-884). Endogenous PML partiallyco-localized with a nuclear form of FlucDM (nFlucDM-GFP), which formedinclusions, but not with the wild-type counterpart (nFlucWT-GFP), whichdisplayed diffuse localization (FIG. 8F). Silencing PML noticeablyelevated the levels of aggregated nFlucDM-GFP (FIG. 8G) and extended thehalf-life of total nFlucDM-GFP protein (FIG. 1L). Taken together, theseresults indicate that PML facilitates the removal of multiple misfoldedproteins in the mammalian cell nucleus.

Recognition of Misfolded Proteins by Distinct Sites on PML

To investigate the mechanism by which PML degrades misfolded proteins,it was first examined whether PML is able to directly recognize theseproteins. For these experiments a pathogenic (103Q) and a nonpathogenic(25Q) Htt fragment, each being fused to glutathione S-transferase (GST),were used. In an in vitro assay with purified recombinant proteins,immobilized FLAG-PML, but not the control protein FLAG-GFP, pulled downGST-Htt 103Q (FIG. 2A), indicating a specific and direct interactionbetween PML and Htt 103Q. FLAG-PML also pulled down GST-Htt 25Q.However, this interaction was substantially weaker than the PML-Htt 103Qinteraction (FIG. 2A). In a reciprocal experiment, immobilized GST-Htt103Q proteins also interacted more strongly with FLAG-PML thanimmobilized GST-Htt 25Q did (FIG. 9A). Hsp70 and Hsp40, which recognizea broad range of misfolded proteins, did not enhance the PML-Htt 103Qinteraction (FIG. 2A). These results suggest that PML can directlyassociate with polyQ proteins and preferentially with the pathogenicform.

It was also examined whether PML selectively binds to denaturedluciferase. 6×His-tagged luciferase that was immobilized on Ni-NTA beadswas either denatured with urea or kept in the native form. Denatured,but not native, luciferase specifically interacted with GST-PML, and theHsp70/Hsp40 system did not enhance this interaction (FIG. 2B). Thus, PMLcan directly recognize misfolded, but not native, luciferase.

To understand the molecular basis for the interaction of PML withmisfolded proteins, it was sought to identify the substrate recognitionsites (SRSs) of PML, as well as the structural features on substratesthat these SRSs discern. It was previously shown that, in a mannerdependent on its length, polyQ and the flanking regions form CCstructures, which facilitate the assembly of polyQ proteins into anoligomeric or aggregated state and also mediate the interaction of polyQproteins with CC-containing proteins (Fiumara et al., 2010, Cell, 143:1121-1135). Thus, it was hypothesized that PML, via its CC region withinthe TRIM/RBCC motif, interacts with pathogenic polyQ proteins. A panelof PML fragments (F1-F5) was constructed, where each fragment eithercontained or lacked the CC region (FIG. 9B). A fragment containing theCC region (F1) interacted with Htt 103Q, while two fragments lackingthis region (F2 and F3) did not (FIG. 9B and FIG. 9C). Moreover, the CCregion alone (F4) bound to Htt 103Q, while deleting this region from theentire PML protein (F5 or ΔCC) greatly diminished this binding. Thus,PML recognizes Htt 103Q almost exclusively through the CC region.Similar to the full-length P-L, PML CC displayed a clear bindingpreference for the pathogenic Htt 103Q to the nonpathogenic Htt 25Q(FIG. 2C). PML CC also strongly interacted with another pathogenic Httconstruct, Htt 52Q (FIG. 2C). Thus, PML CC likely constitutes an SRS(called SRS1).

To test whether PML CC recognizes the homologous CC structure in Httproteins, the residues in Htt 52Q that were predicted to be involved inthe CC formation were mutated, yielding Htt 52Q cc- (FIG. 9D). A similarmutation was previously shown to reduce the formation of the CCstructure in Htt 72Q (Fiumara et al., 2010, Cell, 143: 1121-1135).Indeed, compared to Htt 52Q, Htt 52Q cc- displayed a noticeably reducedpropensity to form aggregates and a substantially weaker interactionwith P-L CC (FIG. 2C). Therefore, PML CC/SRS1 likely interacts with theCC structure on pathogenic Htt proteins.

Given that PML also promotes the degradation of non-polyQ proteins suchas luciferase and TDP-43 (FIG. 1 and FIG. 8 ), it was reasoned that PMLmight contain at least another SRS that could discern non-CC structuralfeatures on misfolded proteins. To test this possibility, the panel ofPML fragments was examined for interaction with denatured luciferase.Although the CC region alone could interact with denatured luciferase,significant levels of interaction were also observed in two fragments(F2 and F5) that lacked this region but contained the C terminus (aa361-633) (FIG. 9B and FIG. 10A). Using additional deletion constructswithin the C terminus (F6-F18, FIG. 9B and FIG. 10B), it was found thata stretch of 63 amino acids (aa 571-633) was sufficient for binding todenatured luciferase. Either NH2- or COOH-terminal deletions of thisstretch abolished the binding (FIG. 10 ). Thus, the last 63 amino acidsof PML likely constitute another SRS (called SRS2).

To investigate the linear sequences in luciferase that can be recognizedby PML SRS2, purified PML SRS2 was used to screen a cellulose-boundpeptide library that represented the complete sequence of luciferase.The library consisted of 180 peptides, each containing 13 amino acidresidues that overlapped adjacent peptides by ten. Similar to chaperonessuch as Hsp70 and ClpB (Rudiger et al., 1997, EMBO J, 16: 1501-1507;Schlieker et al., 2004, Nat Struct Mol Biol, 11: 607-615), PML SRS2 onlybound to a subset of these peptides (FIG. 2D), indicating its ability todistinguish peptides with different amino acid compositions. An analysisof the relative occurrence of all 20 amino acids in PML SRS2-interactingpeptides versus all peptides in the library showed that PML SRS2strongly favored aromatic (Phe, Trp, and Tyr) and positively charged(Arg and Lys) residues, and disfavored negatively charged residues (Aspand Glu) (FIG. 2E). This amino acid preference was similar to that ofClpB, except that SRS2 had an additional preference for Leu and His,which are disfavored by ClpB (Schlieker et al., 2004, Nat Struct MolBiol, 11: 607-615).

For comparison, the binding of PML CC/SRS1 to the peptide library wastested. Consistent with the notion that this region recognizeshigher-order structures instead of linear sequences, PML CC/SRS1 weaklybound to only a few peptides (FIG. 9E). Based on these results, it wasconcluded that PML contains at least two regions that can recognizemisfolded proteins: the CC region within the TRIM/RBCC motif (SRS1) andthe 63 amino acid stretch at its C terminus (SRS2), which can discern CCstructures and exposed peptides enriched in both aromatic and basicamino acids, respectively.

Involvement of SUMOylation in the Degradation of Atxn1 82Q

Experiments were conducted to investigate how PML promotes thedegradation of misfolded proteins upon recognition. Misfolded proteinsassociated with neurodegeneration are frequently modified by SUMO,although the role of this modification remains unclear (Martin et al.,2007, Nat Rev Neurosci, 8: 948-959). Mammalian cells express three majorSUMO proteins, SUMO1-SUMO3. SUMO2 and SUMO3 are nearly identical to eachother in their sequence (collectively called SUMO2/3) and areapproximately 50% identical to SUMO1 (Wilkinson and Henley, 2010,Biochem J, 428: 133-145). The modification of Atxn1 82Q by these SUMOproteins and their involvement in Atxn1 82Q degradation wasinvestigated.

Atxn1 82Q was modified by both exogenous (Riley et al., 2005, J BiolChem, 280: 21942-21948) and endogenous (FIG. 3A, left) SUMO1, and thismodification was weaker than that of Atxn1 30Q (Riley et al., 2005, JBiol Chem, 280: 21942-21948). Atxn1 82Q was also modified by endogenousSUMO2/3 (FIG. 3A, right), and co-localized with GFP-SUMO2/3 in thenucleus (FIG. 3B). The sites in Atxn1 82Q that were conjugated withSUMO1 and SUMO2/3 might be different, because a mutant Atxn1 82Q withimpaired SUMO1 conjugation, Atxn1 82Q (5KR) (Riley et al., 2005, J BiolChem, 280: 21942-21948), showed no defect in SUMO2/3 conjugation (FIG.11A).

Of note, Atxn1 82Q was more strongly modified by endogenous SUMO2/3compared to Atxn1 30Q (FIG. 3C), correlating with the differentresponses of these Atxn1 proteins to PML-mediated degradation (FIG. 1and FIG. 8 ). Similarly, TDP-43 was modified by endogenous SUMO2/3 (FIG.11B). SUMO 2/3 also modified FlucDM, as well as another structurallydestabilized luciferase mutant, FlucSM (Gupta et al., 2011, Nat Methods,8: 879-884). The SUMO2/3 modification of these luciferase mutants wasalso stronger than that of wild-type luciferase (FIG. 11C).

Moreover, proteasome inhibition enhanced the co-localization of Atxn182Q with GFP-SUMO2/3 (FIG. 3B). It also increased SUMO2/3-modified Atxn182Q concurrently with ubiquitinated Atxn1 82Q, but not SUMO1-modifiedAtxn1 82Q (FIG. 3A and FIG. 3D, lanes 2 and 3). Likewise, proteasomeinhibition increased SUMO2/3-modified TDP-43 and luciferase mutants(FIG. 11B and FIG. 11C).

To assess the role of SUMO proteins in the ubiquitination andproteasomal degradation of Atxn1 82Q, SUMO2/3 and SUMO1 were silencedseparately using siRNA. Silencing SUMO2/3, but not SUMO1, effectivelyreduced ubiquitination of Atxn1 82Q (FIG. 3D, lanes 4-7). SilencingSUMO2/3 also raised the levels of Atxn1 82Q, especially the aggregatedform, but not the levels of the control protein GFP (FIG. 11D-FIG. 11F),and it diminished the ability of PML to remove aggregated Atxn1 82Q(FIG. 3E).

SUMO2 and SUMO3 contain an internal SUMOylation consensus site thatenables the formation of polychains. SUMO1 does not contain this site,and when conjugated to the SUMO2/3 chain, it can terminate the chainelongation (Wilkinson and Henley, 2010, Biochem J, 428: 133-145).Therefore, two additional strategies were used to inhibit themodification of Atxn1 82Q by SUMO2/3. First, SUMO1 was overexpressed.This strongly reduced Atxn1 82Q conjugation to SUMO2/3 and, at the sametime, impaired conjugation of Atxn1 82Q to ubiquitin (FIG. 3D, lanes 8and 9) and its degradation by PML (FIG. 3F, left). Second, a SUMO2mutant that was deficient in chain formation, SUMO2 KR, was used.Overexpression of SUMO2 KR effectively reduced the amount ofSUMO2/3-modified Atxn1 82Q species, especially those of high molecularweights. It also reduced ubiquitin-modified Atxn1 82Q species (FIG. 3D,lanes 12 and 13) and blunted the ability of PML to degrade Atxn1 82Q(FIG. 3F, right). Moreover, a SUMOylation-defective Htt mutant, Httex1p97QP(KR) (Steffan et al., 2004, Science, 304: 100-104), was used, and itwas found that it was resistant to the PML-mediated degradation (FIG.1J). Taken together, these results show that ubiquitination anddegradation of Atxn1 82Q and likely other misfolded proteins aredependent on their modification by SUMO2/3.

PML as a SUMO E3 Ligase of Atxn1 82Q

It was previously demonstrated that PML possesses SUMO E3 ligaseactivity that enhances the efficiency and specificity of SUMOylation(Chu and Yang, 2011, Oncogene, 30: 1108-1116). Hence, it was examinedwhether PML promotes SUMOylation of Atxn1 82Q. When co-expressed withAtxn1 82Q in cells, PML strongly increased SUMO2/3 modification of Atxn182Q, both in the absence and in the presence of the proteasome inhibitorMG132 (FIG. 4A). Conversely, silencing PML markedly reducedSUMO2/3-modified Atxn1 82Q under these conditions (FIG. 4B). Similarly,silencing PML reduced SUMO2/3 modification of nFlucDM (FIG. 4C).

To confirm the SUMO E3 activity of PML toward Atxn1 82Q, in vitroSUMOylation assays were performed with purified recombinant proteins. Inthe absence of PML, Atxn1 82Q was weakly modified by SUMO2 (FIG. 4D andFIG. 4E), consistent with previous observations that SUMOylation canproceed in vitro without a SUMO E3 ligase (Wilkinson and Henley, 2010,Biochem J, 428: 133-145). Of note, PML augmented Atxn1 82Q SUMOylationin a dose-dependent manner (FIG. 4D and FIG. 4E). In contrast, a SUMOE3-defective mutant, PML M6 (Chu and Yang, 2011, Oncogene, 30:1108-1116), failed to do so (FIG. 4E and FIG. 11G); PML M6 was alsoineffective at reducing aggregated Atxn1 82Q (FIG. 4F). These resultssuggest that PML is a SUMO E3 ligase of Atxn1 82Q, and that thisactivity is involved in Atxn1 82Q degradation.

A Role for RNF4 in Degrading Misfolded Proteins Proteins conjugated witha poly-SUMO2/3 chain can be recognized and ubiquitinated by RNF4, a RINGdomain ubiquitin ligase with four tandem SUMO-interacting motifs (SIMs)(Sun et al., 2007, EMBO J, 26: 4102-4112). However, the role of RNF4 indegrading misfolded proteins remains undefined. It was found that forcedRNF4 expression strongly reduced the steady-state levels of aggregatedAtxn1 82Q in cell lysates (FIG. 5A), as well as the number of Atxn1 82Qinclusions in the nucleus (FIG. 12A). RNF4 also shortened the half-lifeof aggregated, but not soluble, Atxn1 82Q (FIG. 5B, lanes 1-12; FIG. 5Cand FIG. 12B). Conversely, knocking down endogenous RNF4 with threesiRNAs, individually or in combination, increased total and aggregatedAtxn1 82Q proteins in cell lysates (FIG. 5D, FIG. 12C and FIG. 12D), aswell as Atxn1 82Q inclusions in the nucleus (FIG. 5E). AnsiRNA-resistant form of RNF4 could reverse the effect of RNF4 knockdown(FIG. 12C), indicative of the specificity of the siRNA.

Moreover, both endogenous and exogenous RNF4 proteins normally displayeda diffuse nuclear distribution pattern with minimal or moderateco-localization with Atxn1 82Q inclusions. However, upon proteasomeblockage, RNF4 became highly enriched in Atxn1 82Q inclusions (FIG. 5Fand FIG. 12E), likely reflecting a stalled attempt of RNF4 in clearingAtxn1 82Q. In contrast to its effect on Atxn1 82Q, RNF4 did not reducethe levels of Atxn1 30Q (FIG. 5G). Collectively, these resultsdemonstrate a role for RNF4 in eliminating pathogenic Atxn1 proteins.

To assess a general effect of RNF4 on misfolded proteins, it was testedon Httex1p 97QP, TDP-43, and nFlucDM. Forced expression of RNF4 markedlyreduced Httex1p 97QP, especially the aggregated form, while having amuch weaker effect on Httex1p 97QP(KR) (FIG. 5H). Likewise, forcedexpression of RNF4 decreased the levels of TDP-43 (FIG. 12F), whereassilencing RNF4 augmented the percentage of TDP-43-expressing cells withnuclear inclusions (FIG. 12G and FIG. 12H). Upon proteasome inhibition,endogenous RNF4 became highly enriched in TDP-43 inclusions (FIG. 12I),similar to its accumulation in Atxn1 82Q inclusions under the sameconditions (FIG. 5F). Moreover, silencing RNF4 prolonged the half-lifeof nFlucDM (FIG. 5I). Collectively, these observations suggest that RNF4plays a critical role in the degradation of diverse misfolded proteins.

RNF4 Mediates Ubiquitination and Degradation of SUMO2/3-Modified Atxn182Q

Similar to PML, the ability of RNF4 to eliminate misfolded proteins wasdependent on SUMO2/3, as this ability was compromised in cells devoid ofSUMO2/3, but not in cells devoid of SUMO1 (FIG. 13A). Of note, forcedexpression of RNF4 preferentially reduced SUMO2/3-modified Atxn1 82Q andnFlucDM over the unmodified proteins (FIG. 6A and FIG. 6B). Conversely,silencing RNF4 increased SUMO2/3-modified Atxn1 82Q (FIG. 6C) andenhanced the localization of GFP-SUMO2 to the Atxn1 82Q inclusions (FIG.13B). These results show that RNF4 targets SUMO2/3-modified misfoldedproteins for degradation.

To confirm that RNF4 ubiquitinates SUMO2/3-conjugated misfoldedproteins, an in vitro ubiquitination assay was performed using a mixtureof unmodified and SUMO2-modified Atxn1 82Q proteins (FIG. 6D). In thepresence of increasing doses of RNF4, the SUMO2-modified Atxn1 82Qproteins, which were of relatively low molecular weight (FIG. 6E, lanes1, 6, and 9), were progressively converted to higher-molecular-weightspecies that were also modified by ubiquitin (lanes 2-4, 7-9, and12-14). In contrast, the unmodified Atxn1 82Q protein was notubiquitinated (lanes 1-4). Therefore, RNF4 is a ubiquitin ligase forSUMO2/3-modified, but not unmodified, Atxn1 82Q protein.

RNF4 possesses both ubiquitin ligase and SUMO-binding activities (Sun etal., 2007, EMBO J, 26: 4102-4112). To ascertain the involvement of theseactivities in degrading Atxn1 82Q, RNF4 mutants defective in eitherubiquitin ligase (CS and CS1) or SUMO-binding (SIM^(m)) activity weregenerated (FIG. 13C). CS and CS1, albeit losing their ubiquitin E3activity (FIG. 13D), were still able to co-localize with Atxn1 82Qinclusions (FIG. 6F). SIM^(m), on the other hand, retained a substantiallevel of ubiquitin ligase activity (FIG. 13E), but failed to co-localizewith Atxn1 82Q inclusions (FIG. 6G). Neither of the RNF4 mutant classeswas capable of removing aggregated Atxn1 82Q (FIG. 6H). Collectively,these results suggest that RNF4 binds to SUMO2/3-modified misfoldedproteins via its SIM region and ubiquitinates these proteins via itsligase activity.

Although forced expression of PML led to effective clearance ofaggregated Atxn1 82Q in control cells, this ability was greatlydiminished in RNF4-depleted cells (FIG. 6I). Reciprocally, forcedexpression of RNF4, albeit highly effective in accelerating Atxn1 82Qdegradation in control cells, failed to do so in PML-depleted cells(FIG. 5B, lanes 19-24 versus lanes 7-12; and FIG. 5C). Moreover, inPML-depleted cells, which displayed high Atxn1 82Q levels, silencingRNF4 did not further elevate the levels of Atxn1 82Q (FIG. 13F). Theseresults indicate mutual dependence of PML and RNF4 in the degradation ofAtxn1 82Q.

PML Deficiency Exacerbates Behavioral and Pathological Phenotypes in aMouse Model of SCA1

The results described above revealed a PQC system that degrades Atxn182Q and likely other nuclear misfolded proteins through sequentialPML-mediated SUMOylation and RNF4-mediated ubiquitination. Toinvestigate the physiological role of this system, a mouse model of SCA1(B05), which expresses the Atxn1 82Q transgene (Atxn1^(tg/−)) in thecerebellar Purkinje cells, was used. Resembling human SCA1 patients, B05mice develop ataxia and neurological abnormalities with increasing age(Burright et al., 1995, Cell, 82: 937-948). The loss of RNF4 in miceresults in embryonic lethality (Hu et al., 2010, Proc Natl Acad Sci,107: 15087-15092), precluding the analysis of its effect on B05 mice.However, PML-knockout (PML^(−/−)) mice are viable and appear to developnormally (Wang et al., 1998, Science, 279: 1547-1551). B05 mice werecrossbred with PML^(−/−) and PML-wild-type (PML^(+/+)) mice andlittermates of all genotypes—PML^(+/+), PML^(+/−), and PML^(−/−),PML^(+/+):Atxn1^(tg/−), PML^(+/−):Atxn1^(tg/−), andPML^(−/−):Atxn1^(tg/−)—were compared for both motor performance andneuropathology.

Motor performance—including balance, coordination, and endurance—wasevaluated using a Rotarod apparatus with accelerating speed. Todetermine whether any potential behavioral defects were due to aprogressively diminished capacity, as opposed to a developmentalimpairment, mice at different ages were examined. To rule out theinfluence of the long-term motor memory, only naive animals were used,each being tested for 4 consecutive days.

At 7 weeks of age, all mice performed similarly on the Rotarod (FIG.7A). Although some differences were observed among mice of distinctgenotypes, they were not statistically significant (ANOVA p=0.53),suggesting that PML^(−/−) mice did not have pre-existing impairments intheir motor functions. At 11 weeks of age, all mice lacking the Atxn182Q transgene (PML^(+/+), PML^(+/−), and PML^(−/−)) still showed nostatistical difference in their performance (ANOVA p=0.33) (FIG. 7B),and PML^(+/+) and PML^(+/+):Atxn1^(tg/−) also performed similarly. Theseobservations suggest that either PML deficiency or Atxn1 82Q transgeneexpression alone was insufficient to cause motor defects at this age.Interestingly, PML^(−/−):Atxn^(tg/−) showed severe impairments inRotarod performance compared to either PML^(+/+):Atxn1′¹ or PML^(−/−)mice. Although these three groups of animals were comparable at thebeginning of the 4 consecutive testing days, unlike the other twogroups, PML^(−/−):Atxn1^(tg/−) mice showed minimal improvement overtime. The lack of improvement of PML^(−/−):Atxn^(tg/−) mice on theRotarod was reminiscent of Atxn1^(tg/−) mice at advanced stages (Clarket al., 1997, J Neurosci, 17: 7385-7395). The PML heterozygouscounterparts (PML^(+/−):Atxn^(tg/−) mice) displayed an intermediateimpairment on the Rotarod (ANOVA p=0.0004 for the three Atxn1^(tg/−)groups) (FIG. 7B). Thus, PML deficiency aggravates motor defects of theAtxn1^(tg/−) mice.

The major neuropathological phenotype of the Atxn1^(tg/−) mice is thedegeneration of Purkinje cells, a constituent of the top layer (themolecular layer) of the cerebellar cortex. This degeneration ismanifested initially in the shrinkage of the molecular layer and theatrophy of Purkinje cell dendrites, and later in the loss of Purkinjecell bodies (Burright et al., 1995, Cell, 82: 937-948; Clark et al.,1997, J Neurosci, 17: 7385-7395). At 12 weeks of age, PML^(+/−) andPML^(−/−) mice showed only a slight and statistically insignificantshrinkage in the molecular layers, while PML^(+/+):Atxn1^(tg/−) miceexhibited a discernible shrinkage, compared to PML^(+/+) mice (FIG. 7Cand FIG. 7D). Because PML^(+/+):Atxn1^(tg/−) mice performed similarly onthe Rotarod to PML^(+/+) mice (FIG. 7B), neurodegeneration inPML^(+/+):Atxn1^(tg/−) mice might not have reached a critical threshold.This nonlinear correlation between behavioral and pathologicalphenotypes of the SCA1 transgenic model has been previously observed(Gehrking et al., 2011, Hum Mol Genet, 20: 2204-2212). Importantly,compared to PML^(+/+):Atxn1^(tg/−) mice, PML^(+/−):Atxn1^(tg/−) andPML^(−/−):Atxn1^(tg/−) mice displayed a moderate and a strong furtherreduction, respectively, in the thickness of molecular layer (FIG. 7Cand FIG. 7D). This correlated with worsening performance of theseanimals on the Rotarod (FIG. 7B). Thus, PML deficiency aggravates theshrinkage of the molecular layer in Atxn1^(tg/−) mice.

Dendritic arborization of Purkinje cells was also examined byimmunofluorescence staining with an antibody against the Purkinjecell-specific protein calbindin. At 12 weeks of age, the fluorescenceintensity of Purkinje cell dendrites in all groups containing the Atxn182Q transgene was reduced to very low levels that precluded precisecomparison (FIG. 14A and FIG. 14B). Of note, compared to PML^(+/+)littermates, PML^(−/−) mice already showed a strong reduction indendritic arborization of Purkinje cells, while PML^(+/−) mice showed anintermediate reduction (FIG. 14A and FIG. 14B). These results indicatethat PML itself has a role in protecting against neurodegeneration.

Despite the thinning of the molecular layer and the loss of Purkinjecell dendrites that were associated with PML deficiency, no significantdifference in Purkinje cell population was observed among 12-week-oldanimals of different genotypes (FIG. 14C). At 1 year of age, PML^(−/−)mice displayed only a mild (11.0%) and statistically insignificant(p=0.107) reduction in the number of Purkinje cells compared toPML^(+/+) mice, while PML^(+/+):Atxn1^(tg/−) mice displayed a noticeablereduction (FIG. 7E and FIG. 7F). Of note, PML^(−/−):Atxn1^(tg/−) miceshowed a significant further reduction in Purkinje cell density comparedto PML^(+/+):Atxn1^(tg/−) mice (˜24%, p=0.0023), andPML^(+/−):Atxn1^(tg/−) mice showed an intermediate cell loss (FIG. 7Eand FIG. 7F). Again, these results demonstrate that PML deficiencyworsens the neuropathological defects caused by the Atxn1 82Q transgene.

Neurodegeneration of B05 mice is accompanied by the formation ofubiquitin-positive Atxn1 82Q inclusions in Purkinje cells (Clark et al.,1997, J Neurosci, 17: 7385-7395). To determine the effect of PML onAtxn1 82Q nuclear inclusions, Purkinje cells with these inclusions werequantified in mice at 12 weeks of age. PML deficiency alone did notresult in the formation of aggregates (FIG. 14D), but it significantlyincrease the number of aggregate-containing Purkinje cells in Atxn1 82Qtransgenic mice (FIG. 7G and FIG. 7H). Collectively, these resultssuggest that endogenous PML plays a role in preventing accumulation ofmisfolded proteins in SCA1 animals and suppressing the progression ofthis neurodegenerative disease.

PQC System that Degrades Misfolded Proteins

Presented herein is evidence for a PQC system that degrades misfoldedproteins in mammalian cell nuclei. This system comprises a recognitionbranch, PML, which selectively binds to misfolded proteins and marksthese proteins with poly-SUMO2/3 chains, and an effector branch, RNF4,which ubiquitinates SUMOylated misfolded proteins and targets them forproteasomal degradation. This relay system likely provides a criticallink between misfolded proteins and the proteasome in mammalian cells,and it may play an important role in the protection againstneurodegeneration and other proteopathies (FIG. 7I).

Selective Recognition of Misfolded Proteins by PML

The exquisite selectivity of this system resides in PML, which containsat least two SRSs. SRS1, consisting of the CC region within theTRIM/RBCC motif, favors CC structures on pathogenic polyQ proteins andperhaps other misfolded proteins. SRS2, consisting of the C-terminal 63amino acids, recognizes short peptides enriched in both aromatic (Phe,Trp, and Tyr) and positively charged (Arg and Lys) amino acids. SRS2 issimilar to the bacterial Hsp100 ClpB (Schlieker et al., 2004, Nat StructMol Biol, 11: 607-615), except that SRS2 also favors peptides containingLeu, a residue that is often exposed in misfolded proteins and isengaged by Hsp70 (Rudiger et al., 1997, EMBO J, 16: 1501-1507). Thus,SRS2 displays a hybrid substrate specificity of ClpB and Hsp70. Theseobservations indicate that PML can recognize structures or regions thatare commonly found in misfolded proteins.

A Role for SUMOylation in Degrading Misfolded Proteins

Conjugation to SUMO is a major posttranslational modification, occurringon numerous proteins and vital to most eukaryotic life. Yet, beyond thegeneralization that it alters protein-protein interactions, thephysiological function of SUMOylation remains elusive (Wilkinson andHenley, 2010, Biochem J, 428: 133-145). A prominent feature of thePML-RNF4 system is the involvement of SUMO2/3 modification prior toubiquitination (FIG. 3 , FIG. 4 , and FIG. 11 ). It was observedpreviously that conjugation of SUMO2/3 to cellular proteins is markedlyenhanced by protein-denaturing stresses (Saitoh and Hinchey, 2000, JBiol Chem, 275: 6252-6258). The evidence presented in the current studyprovides an explanation for this observation, and suggests that aprincipal physiological function of SUMO2/3 modification is likely tofacilitate the degradation of misfolded proteins, acting in concert withubiquitination.

SUMO conjugation enhances protein solubility (Panavas et al., 2009,Methods Mol Biol, 497: 303-317). Because aggregated proteins cannot beeffectively degraded by the proteasome (Verhoef et al., 2002, Hum MolGenet, 11: 2689-2700), enhancing protein solubility may be a beneficialeffect conferred by PML prior to ubiquitination. Moreover, the extent ofSUMOylation may enable the “triage decision” as to whether a givenmisfolded protein is selected for refolding or degradation. Consistentwith this notion, conjugation to a single SUMO appears to be sufficientto enhance protein solubility (Panavas et al., 2009, Methods Mol Biol,497: 303-317), and thus may facilitate refolding. In contrast,conjugation to SUMO2/3 chains is needed for effective recognition by thefour tandem SIMs on RNF4 for ubiquitination and degradation (Tatham etal., 2008, Nat Cell Biol, 10: 538-546). Such chains may form afterunsuccessful refolding attempts.

SUMOylation of misfolded proteins has been reported to either promote orinhibit neurodegenerative diseases (Martin et al., 2007, Nat RevNeurosci, 8: 948-959). These seemingly contradictory observations may bereconciled by the distinct functions of SUMO1 and SUMO2/3 in the removalof misfolded proteins (FIG. 3 ), and by the dichotomy between thefunctions of SUMOylation: enhancing solubility of an abnormal protein(which may enhance its toxicity) and promoting its degradation. Thus,the outcome of elevated SUMOylation likely depends on whether it can bematched by the cellular degradative capacity.

A Potential Major PQC System

Proteins in the nucleus may harbor mutations or sustain acute andchronic damages, as proteins elsewhere do. The highly crowdedenvironment of the nucleus likely makes it especially challenging tomaintain protein quality. The ubiquitin-proteasome pathway is expectedto be the main degradative system in the nucleus, where autophagy is notknown to operate. Previous studies have implicated a few ubiquitinligases, such as yeast San1 and Doa10 and mammalian UHRF-2 and E6-AP, inthe degradation of nuclear misfolded proteins (Cummings et al., 1999,Neuron, 24: 879-892; Deng and Hochstrasser, 2006, Nature, 443: 827-831;Gardner et al., 2005, Cell, 120: 803-815; Iwata et al., 2009, J BiolChem, 284: 9796-9803). Nevertheless, the predominantly nuclearlocalization of PML, along with the potent effect of PML and RNF4 ondiverse misfolded nuclear proteins, suggests that the PML-RNF4 system islikely a major PQC system in mammalian cell nuclei.

The TRIM family of proteins is shared among metazoans, fromapproximately 20 members in C. elegans to over 70 in mice and humans(Ozato et al., 2008, Nat Rev Immunol, 8: 849-860). It was previouslydemonstrated that at least several other TRIM proteins also possess SUMOE3 activity (Chu and Yang, 2011, Oncogene, 30: 1108-116). Given theirlocalization to the cytoplasm in addition to the nucleus (Ozato et al.,2008, Nat Rev Immunol, 8: 849-860), it is speculated that TRIM proteinsalso participate in PQC in the cytoplasm. The rapid expansion of theTRIM proteins during evolution might in part be a response to theincreasing complexity of managing protein quality in cells oflonger-living animals.

RNF4 is conserved among vertebrates (Sun et al., 2007, EMBO J, 26:4102-4112). SUMO-dependent ubiquitin ligases are also present in loweukaryotic species (Sun et al., 2007, EMBO J, 26: 4102-4112), and areinvolved in the degradation of at least one mutant yeast transcriptionfactor (Wang and Prelich, 2009, Mol Cell Biol, 29: 1694-1706). Thus, itis also possible that systems analogous to the PML-RNF4 system may playa role in maintaining protein quality in these organisms.

The PML-RNF4 System and Neurodegeneration

PML^(−/−) mice have been extensively characterized for a variety ofphenotypes including tumorigenesis (Wang et al., 1998, Science, 279:1547-1551). The present study indicates a role for PML in protectionfrom neurodegeneration (FIG. 7 and FIG. 14 ). Neurodegenerativedisorders including SCAs and HD are usually late-onset diseases.Accumulating evidence suggests a progressive decline in PQC during aging(Balch et al., 2008, Science, 319: 916-919). The strong effect of thePML-RNF4 on pathogenic proteins associated with SCA1, HD, and ALS and ofPML deficiency on the progression of the SCA1 mouse model, along withthe accumulation of PML in neuronal inclusions in patients with variousneurodegenerative diseases (Skinner et al., 1997, Nature, 389, 971-974;Takahashi et al., 2003, Neurobiol Dis, 13: 230-237), suggests thatinsufficiency or dysfunction of the PML-RNF4 system may have a role inthese diseases. Thus, the PML-RNF4 system and analogous systems would bevaluable targets in their treatment.

Example 2: TRIM Proteins can Recognize Misfolded Proteins and PromoteTheir Degradation

The tripartite motif-containing (TRIM) family consists of a large numberof proteins in metazoan cells, ranging from approximately twenty in C.elegans to over seventy in mice and humans. These proteins share attheir N-termini the characteristic TRIM or RBCC motif, which iscomprised of a RING domain, one or two B-boxes (which, like the RINGdomain, a coordinated by zinc ions), and a coiled coil region. This isfollowed by C-terminal region that are much more variable among TRIMproteins and contains distinct motifs (Hatakeyama, 2011, Nat Rev Cancer,11: 792-804; Ozato et al., 2008, Nat Rev Immunol, 8: 849-860). TRIMproteins modulate a range of cellular processes including those thatprotect against cancer and viral infection. Biochemically, a number ofTRIM proteins exhibit ubiquitin E3 ligase activity, which is attributedto the RING domain within the TRIM/RBCC region. In addition, at leastseveral TRIM proteins possess E3 ligases for protein conjugation to SUMO(small ubiquitin-like modifier). However, an outstanding issue hasremained as to the substrates of the TRIM family of SUMO E3.

As described above, it was demonstrated that PML (promyelocytic leukemiaprotein; also known as TRIM19) plays a critical role in the eliminationof misfolded proteins. PML was initially identified as the product of agene involved in the t(15;17) chromosomal translation that is associatedwith the majority of acute promyelocytic leukemia. It is the majorstructural and the namesake component of the PML nuclear bodies. It wasshown that PML is able to specifically bind to and promote thedegradation of a range of misfolded protein. Via distinct regions, PMLcan discern common features found in misfolded proteins, includingpeptides enriched in aromatic amino acid residues and coiled coilstructures. PML then tags misfolded proteins with poly-SUMO2/3 chainsthrough its SUMO E3 activity. This permits modified misfolded proteinsto be recognized by the SUMO-targeted ubiquitin ligase (STUbL) RNF4,which ubiquitinates misfolded proteins and target them for with theconsequential degradation in the proteasome. The role of PML in proteinquality control is important for the protection againstneurodegenerative diseases, as PML deficiency exacerbates behavioral aswell as neuropathological phenotypes of a mouse model of spinocerebellarataxia type 1 (SCA1), a progressive and lethal disease caused by theexpansion of a polyglutamine (polyQ) stretch in ataxin-1. Given theexistence of a large number if TRIM proteins, the results obtained usingPML raises an important question as to whether other TRIM proteins, likePML, are able to recognize and degrade misfolded proteins. In theexperiments presented herein, a panel of TRIM proteins is analyzed andit is observed that the ability to recognize and degrade misfoldedproteins is prevalent among TRIM proteins, indicating a critical rolefor this family in protein quality control in metazoan cells.

The materials and methods employed in these experiments are nowdescribed.

Plasmids

FLAG-TRIM27, FLAG-TRIM32, and FLAG-TRIM5δ were made in pRK5 by PCR.Templates for PCR amplification were purchased from Open Biosystems, andthe corresponding gene accession numbers are BC013580, BC003154 andCV029096, respectively. All three genes are of human origin. Thefollowing plasmids were previously described: FLAG-PML (isoform IV) (Chuand Yang, 2011, Oncogene, 30: 1108-116); Atxn1 82Q-GFP, FLAG-Atxn1 82Q,and HA-Httex1p 97QP (Guo et al., 2014, Mol Cell, 55(1): 15-30);FLAG-TRIM11 (Ishikawa et al., 2006, FEBS Lett, 580: 4784-4792);FLAG-TRIM22 (the long form) (Barr et al., 2008); HA-TRIM39 (Lee et al.,2009, Exp Cell Res, 315: 1313-1325); HA-tagged TRIM1, 2, 3, 4, 5, 6, 8,9, 10, 11, 12, 13, 14, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, and 32 (Reymond et al., 2001, EMBO J, 20: 2140-2151; Uchil et al.,2008, 2008, PLoS Pathog, 4: e16); and the remaining TRIM expressionplasmids, expressing proteins with either an N-terminal HA-tag orC-terminal V5 tag (Versteeg et al., 2013, Immunity, 38: 384-398). Foranalyzing the effect of TRIM proteins on the levels of Atxn1 82Q andHttex1p 97QP, Trim 11 (NM_145214.2), Trim15 (NM_033229.2), Trim28(NM_005762.2), Trim34 (NM_021616.5), Trim39 (NM_021253.3), Trim42(NM_152616.4), Trim43 (NM_138800.1), Trim65 (NM_173547.3), Trim67(NM_001004342.3), Trim70 (NM_001037330.1), Trim71 (NM_001039111.2)_andTrim75 (NM_001033429.2) were constructed into pcDNA 3.1(−) vectorcontaining a 5′-HA tag. All the other Trim plasmids were obtained(Versteeg et al., 2013, Immunity, 38: 384-398).

siRNAs

SUMO2/3 siRNAs (Santa Cruz sc-37167) was a pool of three different siRNAduplexes with the sense strand sequences of 5′-CCCAUUCCUUUAUUGUACA-3′(SEQ ID NO: 157), 5′-CAGAGAAUGACCACAUCAA-3′ (SEQ ID NO: 158), and5′-CAGUUAUGUUGUCGUGUAU-3′ (SEQ ID NO: 159).

TRIM27 siRNA was purchased from Qiagen, with the sense strand sequencesbeing 5′-AACTCTTAGGCCTAACCCAGA-3′ (SEQ ID NO: 162).

Cell Culture and Transfection

HeLa cells were obtained from ATCC. PML^(+/+) and PML^(−/−) MEF cellswere derived from the embryos of mice with the corresponding genotypes.Cells were maintained in standard culture conditions. DNA plasmids weretransfected into cells using Lipofectamine 2000, and siRNAs weretransfected into cells in two rounds on consecutive days using eitherLipofectamine 2000 or RNAiMAX (Invitrogen), according to themanufacturer's instructions. When both DNA and siRNA were transfected,DNA was transfected a day after the second round of siRNA transfection.MG132 (Sigma) was added 24 hours after the last transfection at 7.5-10μM (final concentration) for 4-5 hours.

Immunofluorescence

Cells cultured on coverslips were fixed with 4% paraformaldehyde for 15minutes, permeabilized with 0.2% Triton X-100 for 15 minutes, andincubated sequentially with primary and secondary antibodies. Primaryantibodies were anti-HA, anti-FLAG (mouse mAb M2, 1:2,000) (Sigma), andanti-TRIM27. Secondary antibodies were FITC-conjugated anti-mouse,anti-rabbit (Zymed), and anti-goat (Invitrogen) IgGs; TexasRed-conjugated anti-mouse and anti-rabbit IgGs (Vector labs); andRhodamine Red-X conjugated anti-goat (Jackson ImmunoResearch Labs).Afterwards, cells were mounted with medium containing DAPI (VectorLabs), and the images were acquired with a Nikon Eclipse E800 or OlympusIX81 microscope.

Cell Lysate Fractionation, Western Blot, and Filter Retardation Assay

Samples were prepared as described (Guo et al., 2014, Mol Cell, 55(1):15-30). Briefly, cells were lysed on ice in NP-40 lysis buffer (50 mMTris, pH 8.8, 100 mM NaCl, 5 mM MgCl₂, 0.5% NP-40, 2 mM DTT)supplemented with 250 IU/ml benzonase (Sigma), 1 mM PMSF, 1× completeprotease cocktail (Roche), and 20 mM N-Ethylmaleimide (NEM; Sigma). Celllysates were centrifuged at 13,000 rpm for 15 minutes at 4° C. Thesupernatant, containing NP-40-soluble (NS) proteins, was analyzed bySDS-PAGE and Western blot. The pellet was resuspended in the pelletbuffer (20 mM Tris, pH 8.0, 15 mM MgCl₂, 2 mM DTT) supplemented with 250IU/ml benzonase, 1 mM PMSF, 1×complete protease cocktail, and 20 mM NEM.The pellet fraction was boiled in 2% SDS plus 50 mM DTT and was resolvedby SDS-PAGE. Proteins entering the gel (SDS-soluble, SS) were detectedby Western blot. For filter retardation (dot blot) assay, a portion ofthe boiled pellet was applied to a membrane filter with 0.2 μm poresize, and the SDS-resistant (SR) aggregates retained on the filter wasanalyzed by immunoblotting. Primary antibodies were: anti-HA (rabbit,Y-11, 1:500) (Santa Cruz Biotechnology); anti-FLAG (mouse, M2, 1:7,500)and anti-actin (rabbit, 1:10,000) (Sigma); anti-GFP (mouse, 1:4,000)(Clonetech); and SUMO2/3 (rabbit, 1:250, Abgent). The secondaryantibodies were either conjugated to HRP (Santa Cruz Biotechnology), orlabeled with IRD Fluor 800 or IRD Fluor 680 (LI-COR, Inc.). Westernblots were developed using ECL reagents and analyzed using ImageJ, orscanned with the Odyssey infrared imaging system, and analyzed usingImage Studio Lite (LI-COR, Inc.).

Protein Purification and In Vitro SUMOylation Assays

FLAG-TRIM27 and HA-Atxn1 82Q-FLAG were expressed in 293T cells andpurified by anti-FLAG M2 beads (Sigma) as previously described (Tang etal., 2006, Nat Cell Biol, 8: 855-862; Tang et al., 2004, J Biol Chem,279: 20369-20377) with modifications. Cells were lysed in IP-lysisbuffer (50 mM Tris, pH 7.5, 150 mM NaCl, 0.5% Triton X-100, 0.5% NP-40and 2 mM DTT) supplemented with 1 mM PMSF and 1×complete proteasecocktail. For TRIM27 purification, IP-lysis buffer was also supplementedwith 20 μM ZnCl2. The lysates were incubated with anti-FLAG M2 beads at4° C. for 4 hours to overnight. M2 beads were washed with IP-lysisbuffers containing 0, 0.5, and 1 M KCl, and with the elution buffer (50mM Tris, pH 7.5, 150 mM NaCl, and 2 mM DTT). The bound proteins wereeluted in the elution buffer containing 0.1-0.3 mg/ml 3×FLAG peptide(Sigma).

Other components for in vitro SUMOylation reactions were purchased fromBoston Biochem. In vitro SUMOylation assays were performed at 37° C. for1.5 hours in 30 μl reaction buffer (50 mM Tris pH 7.5, 5.0 mM Mg2+-ATP,and 2.5 mM DTT) containing purified HA-Atxn1 82Q-FLAG (600 ng/200 nM),FLAG-TRIM27, SAE1/SAE2 (125 nM), Ubc9 (1 μM), His-SUMO2 (25 μM), and BSA(0.1 μg/ml). The reaction mixtures were denatured by the addition of 30μl IP-lysis buffer containing 2% SDS and 50 mM DTT and heating at 95° C.for 10 minutes. One aliquot of the heated reaction mixes were saved forWestern blot analysis, and the rest were diluted 20-fold in IP-lysisbuffer without SDS. HA-Atxn1 82Q-FLAG was immunoprecipitated by anti-HAbeads (Roche) and analyzed for SUMO2/3 modification using ananti-SUMO2/3 antibody.

The results of the experiments are now described.

Co-Localization of TRIM27, TRIM32, and TRIM5δ with Pathogenic Ataxin-1and Huntingtin Proteins

It was previously showed that PML/TRIM19 can recognize and promote thedegradation of various nuclear misfolded proteins including Atxn1 82Q, apathogenic ataxin 1 protein with a stretch of eight-two glutamine thatis associated with spinocerebellar ataxia type 1 (SCA1) (Guo et al.,2014, Mol Cell, 55(1): 15-30). The TRIM family of proteins in humans andmice consists of over seventy members that can be distinguished based onstructural features of the region C-terminal to the conserved TRIM/RBCCmotif (Ozato et al., 2008, Nat Rev Immunol, 8: 849-860). The majority ofTRIM proteins contain in this region one or more conserved domains, themost common of which include the PRY-SPRY domain (present in ˜40 TRIMproteins) and multiple NHL domains (present in 4 TRIM proteins). Inaddition, several TRIM proteins do not contain a recognizable motif inthe C-terminal region. To examine whether other human TRIM proteins,like PML, are able to recognize misfolded proteins, TRIM27 (with aPRY-SPRY domain), TRIM32 (with multiple NHL domains), and TRIM5δ (ashort splicing variant of TRIM5 with no known domain) were first chosen.When expressed in HeLa cells, these three TRIM proteins displayedoverlapping yet distinct cellular localization patterns: TRIM27 andTRIM32 were localized in both the cytoplasm and the nucleus, whileTRIM5δ was localized only in the cytoplasm. Nevertheless, all threeproteins are concentrated in the speckled bodies in their respectivecompartment(s) (FIG. 15A).

Experiments were conducted to examine the co-localization of TRIM27,TRIM32, and TRIM5δ with Atxn1 82Q, as well as with a fragment of thehuntingtin protein (Htt) containing a stretch of ninety-seven glutamines(Httex1p 97Q), which is associated with HD. Atxn1 82Q, which wasexpressed as a fusion of enhanced green fluorescence protein (GFP),formed inclusions only in the nucleus, while HA-tagged Httex1p 97QPformed inclusions in both the nucleus and cytoplasm (Guo et al., 2014,Mol Cell, 55(1): 15-30) (FIG. 15A and FIG. 15B). Exogenous TRIM27 andTRIM32 co-localized with Atxn1 82Q-GFP inclusion in the nucleus (FIG.15A) and with HA-Httex1p 97QP inclusions in both the nucleus andcytoplasm (FIG. 15B and FIG. 15C). Moreover, endogenous TRIM27 alsoco-localized with Atxn1 82QGFP inclusion (FIG. 15D). Exogenous TRIM5δco-localized only with the cytoplasmic HA-Httex1p 97QP inclusions (FIG.15B and FIG. 15C). Thus, despite the differences in their C-terminalsequence, TRIM27, TRIM32, and TRIM5δ are able to recognize misfoldedprotein formed in their respective cellular compartment(s).

TRIM27, TRIM32, and TRIM5δ Reduce the Levels of Both Insoluble andSoluble Atxn1 82Q proteins

To examine whether these TRIM proteins are able to reduce the levels ofmisfolded proteins, each of them was expressed with FLAG-tagged Atxn182Q in HeLa cells. The levels of FLAG-Atxn1 82Q in cell lysates thatwere NP40-soluble (soluble or NS) and NP-40-insoluble, but SDS-soluble(aggregated or SS), were analyzed. Of note, each TRIM protein was ableto reduce the levels of soluble and aggregated Atxn1 82Q protein (FIG.16A and FIG. 16B). TRIM27 and TRIM32 also decreased the levels of Atxn182Q protein that were resistant to both NB-40 and SDS (SR), which weredetected by a filter retardation assay and likely represented P-amyloidstructure (see below).

When expressed at similar levels, all three TRIM proteins, especiallyTRIM32, showed stronger activity than PML in reducing the levels ofsoluble Atxn1 82Q (FIG. 16A). Moreover, while the activity of TRIM27 andTRIM5δ was somewhat weaker than, the activity of TRIM32 in reducingaggregated Atxn1 82Q was comparable to that of PML (FIG. 16A and FIG.16B). TRIM27 was chosen for further analysis. The expression ofendogenous TRIM27 was knocked down using siRNA, which led to asignificant increase in the levels of both soluble and aggregated Atnx182Q proteins (FIG. 16C). Together, these results suggest that similar toPML, TRIM27, TRIM32, and TRIM5δ are capable of removing misfoldedproteins. In contrast to these TRIM proteins, PIASy, a member of thePIAS family of SUMO E3s, was unable to reduce the levels of eithersoluble or aggregated Atxn1 82Q (FIG. 16D).

The Effect of TRIM27 and TRIM32 on Atxn1 82Q is Independent of PML

TRIM27 is partially co-localized in PML nuclear bodies (Cao et al.,1998, J Cell Sci, 111(Pt 10): 1319-1329) (FIG. 17A). To examine whetherTRIM27 and the other nucleus-localized TRIM protein, TRIM32, rely on PMLto degrade misfolded protein, PML-wild type (PML^(+/+)) andPML-deficient (PML^(−/−)) mouse embryonic fibroblasts (MEFs) were used.Despite the co-localization of TRIM27 with the P-L nuclear bodies,TRIM27 was present in the Atxn1 82Q aggregates even in the absence ofPML (FIG. 17B). The levels of SDS-insoluble Atxn1 82Q aggregates weremarkedly higher in PML^(−/−) compared to PML^(+/+) MEFs (FIG. 17C),consistent with a role for PML in removing Atxn1 82Q (Guo et al., 2014,Mol Cell, 55(1): 15-30). Re-introducing PML decreased the levels of theaggregate Atxn1 82Q. Of note, TRIM27 and TRIM32 were as effective as PMLin reducing aggregated Atxn1 82Q in both PML^(+/+) and PML^(−/−) cells(FIG. 17C). Together, these results suggest that TRIM27 and TRIM32 caneliminate Atxn1 82Q independently of PML.

TRIM27, TRIM32, and TRIM5δ Target Atxn1 82Q for Proteasomal Degradationin a SUMO2/3-Dependent Manner

It was previously found that PML promotes proteasomal degradation ofmisfolded proteins via its SUMO E3 activity (Guo et al., 2014, Mol Cell,55(1): 15-30). When cells were treated with the proteasome inhibitorMG132, the ability of TRIM27, TRIM32, and TRIM5δ to reduce soluble andespecially insoluble Atxn1 82Q protein was significantly impaired,suggesting that these three TRIM proteins also target Atxn1 82Q forproteasomal degradation (FIG. 18A-FIG. 18C). In addition, whenendogenous SUMO2/3 was knocked down with siRNAs, TRIM27, TRIM32, andTRIM5δ could no longer effectively reduce the levels of Atxn1 82Q (FIG.18D-FIG. 18F). Hence, these TRIM proteins also rely on SUMO2/3 indegrading Atxn1 82Q.

Using TRIM27 as an example, it was next examined whether TRIM proteinsother than PML can act as SUMO E3 ligases for Atxn1 82Q. When incubatedwith SUMOylation reaction components, including SUMO E1 (SAE1/SAE2), E2(Ubc9), SUMO2, and ATP, Atxn1 82Q was minimally conjugated to SUMO2.However, conjugation of Atxn1 82Q to SUMO2 was enhanced in a TRIM27dose-dependent manner (FIG. 18G), suggesting that TRIM27 is a SUMO E3for Atxn1 82Q.

Co-Localization with Misfolded Proteins is a Prevalent Property of TRIMProteins

Prompted by these observations, the remaining TRIM proteins were testedfor their ability to recognize Atxn1 82Q. With the exception of two(TRIM12 and TRIM30), which are present in mice but not in humans, allthe other TRIM proteins are of human origin. Each TRIM was tagged witheither an HA, Flag, or V5 epitope, and was co-expressed with Atxn182Q-EGFP in HeLa cells.

A previous survey of a subset of TRIM proteins showed that theseproteins identify with compartments in both the cytoplasm and nucleus(Reymond et al., 2001, EMBO J, 20: 2140-2151). Among the TRIM proteinstested here, eleven (TRIM42, 43, 53, 59-61, 67, 70-72, and 75) could notbe detected by immunofluorescence. Among the remaining sixty-three TRIMproteins, five of them (TRIM22, 28, 33, 65, and 66) were localizedexclusively in the nucleus, a localization pattern similar to PML.However, the possibility that certain isoforms of these TRIM proteinsthat were not tested here may be present in the cytoplasm cannot beexcluded. For example, such cytoplasmic isoforms have been shown forPML. Twenty-seven TRIM proteins (TRIM1-5, 7, 9, 10, 13, 18, 20, 24, 25,29, 34, 36, 37, 39, 45-47, 50, 54, 63, 69, and 76) were localized mainlyor exclusively in the cytoplasm. Twenty-seven TRIM proteins (TRIM6, 8,11, 12, 16, 21, 23, 27, 30-32, 35, 38, 40, 44, 48, 49, 51, 52, 55, 56,58, 62, 64, 68, 73, and 74) were present in a substantially amount inboth the nucleus and cytoplasm. A number of the TRIM proteins eitherformed speckled or filamentous structures in the nucleus or thecytoplasm, others were localized diffusedly, and a few of them displayedperinuclear localization. Often, a TRIM protein exhibited thecombination of these localization patterns either in the same ordifferent cells (FIG. 19 and Table 2).

Fourteen TRIM proteins (TRIM6, 8, 11, 19, 21, 22, 27, 28, 30, 32, 33,35, 38, and 51), including PML/TRIM19, co-localized with the nuclearAtxn1 82Q inclusions in a substantial number of cells (FIG. 19 and Table2), representing nearly 43% of the thirty-two TRIM proteins that werepresent either partially or exclusively in the nucleus. These TRIMproteins are from distinct subgroups with different C-terminalsequences. Six proteins (TRIM6, 11, 21, 22, 35, and 38), like TRIM27,are members of the subgroup IV, containing a SPRY motif that is oftenpreceded by a PRY motif. TRIM8, like PML, is a member of the group V,containing no known domains. TRIM28 and TRIM33 are members of group VI,containing a PHD-BR motif. TRIM32 belongs to the subgroup VII, with afive NHL repeats. TRIM51 is considered a TRIM-like protein, lacking thetwo B-boxes but containing the RING domain and the coiled-coil region;it also contains a SPRY domain, like members of the subgroup IV.Together, these results show that a substantial number of TRIM proteins,despite the divergence in their C-terminus, possess the ability torecognize misfolded proteins.

Degradation of Misfolded Proteins Mediated by Other TRIM Proteins

To examine the role of TRIM proteins in protein quality control, allhuman TRIM proteins except for TRIM53 (pseudogene) and TRIM57 (same asTRIM59), as well as TRIM12 and TRIM30 (of mouse origin), were tested forthe ability to degrade Atxn1 82Q. Thirty-five of the human TRIM proteins(TRIM3, 4, 5, 6, 7, 9, 11, 13-17, 19, 20, 21, 24, 25, 28, 29, 34, 39,43-46, 49, 50, 52, 58, 59, 65, 67, 70, 74, and 75) and mouse TRIM30 wereable to reduce the levels of NS and/or SS fractions of Atxn1 82Q todifferent extents (FIG. 20A and Table 2). Several TRIM proteins showedstrong activity, including TRIM4, 5, 9, 11, 16, 17, 20, 30, 39, 43, 65,70, 75 (FIG. 20A and Table 2), and the one with strongest activityappeared to be TRIM11 (FIG. 16A, FIG. 20A and Table 2). Of note, TRIM27and TRIM32, which were shown above to be able to reduce Atxn1 82Q, didnot display an effect in this assay. This difference was likely due tothe expression levels. In the experiments described above, TRIM27 andTRIM32 were cloned into the plasmid pRK5. But in the experimentsdescribed in this section, TRIM27 and TRIM32 were cloned into pcDNA.Stronger expression from the pRK5 plasmids were consistently observed ascompared to expression from the pcDNA plasmid. Therefore, even for theones that did not display an activity to degrade Atxn1 82Q, they mightdo so when their expression levels were elevated. It is thereforeconcluded that the ability to promote degradation of Atxn1 82Q isprevalent among TRIM proteins.

Of note, a few TRIM proteins enhanced, rather than inhibited, theexpression of Atxn1 82Q, including TRIM26, 33, 42, 47, 48, 66, 69, and76. This suggests a diverse effect of different TRIM proteins on Atxn182Q.

In parallel, the effect of TRIM proteins on Httex1p 97QP was alsoexamined (FIG. 20B). Only a few TRIM proteins were able to reduce thelevels of Httex1p 97QP in the NS and/or SS fractions, including TRIM3,11, 30, 68, 74, and 75. The majority of the TRIM proteins were able toincrease the levels of Httex1p 97QP, including TRIM1, 4, 6-10, 12-15,21, 23-28, 32-39, 41-47, 49-51, 54-56, 58, 60-67, 69-73, 76, and 77.Unlike Atxn1 82Q, only a small fraction of cells expressing Httex1p 97QPcontained inclusion. Consistently, the portion of Httex1p 97QP proteinin the SS fraction was very low compared to the portion of Atxn1 82Q inthe same fraction. Also, in the previous study, PML (cloned in the pRK5plasmid) was able to reduce the levels of Httex1p 97QP, while here PML(cloned in pcDNA) was not. Thus, the effect of TRIM proteins on Httex1p97QP, like their effect of Atxn1 82Q, might also be influenced by theirexpression levels. These results suggest different effects of TRIMproteins on different misfolded proteins, which, among others, can beinfluenced by their expression levels.

TRIM Proteins

Previously it has been shown that PML is able to eliminate a range ofmisfolded proteins presented in the nucleus of mammalian cells. Theexperiments presented herein systematically analyzed nearly all TRIMproteins and find that unprecedented large number of them can recognizemisfolded proteins. Still, this number is likely to be an underestimate,because a single misfolded protein, Atxn1 82Q, was mainly used. At leasttwo substrate recognition sites (SRSs) have been identified in P-L, thecoiled-coil region within the RBCC motif and the region comprising thelast sixty amino acids. These SRSs can discern coiled-coil structuresand peptides enriched in aromatic acid residues (Phe, Trp, and Tyr),respectively, which are found in some denatured proteins. TRIM proteinsare most divergent in their C-terminal region (Hatakeyama, 2011, Nat RevCancer, 11: 792-804; Ozato et al., 2008, Nat Rev Immunol, 8: 849-860).It is likely that other TRIM proteins may process specific ability torecognized misfolded proteins of distinct structural features. Also, itis likely that many TRIM proteins that can recognize misfolded proteinsin the cytoplasm. Hence, the present observations underscore thecritical importance of this large family in protein quality control.

Of note, TRIM5δ was able to promote Atxn1 82Q degradation despite of itscytoplasmic localization. It is possible that TRIM5δ can recognizesoluble, misfolded Atxn1 82Q in the cytoplasm before it is imported intothe nucleus. Also, TRIM27 and TRIM32 show strong ability to degradesoluble Atxn1 82Q, while PML shows less activity. This might be relatedto the fact that, unlike PML, TRIM27 and TRIM32 are partially localizedto the cytoplasm, where Atxn1 82Q protein (and virtually all the otherproteins) is generated. Hence, by recognizing misfolded proteins thatare destined to the nucleus, the cytoplasmic TRIM proteins may play animportant role in protein quality control in the nucleus.

PML degrades misfolded proteins in a manner that is dependent on itsSUMO E3 activity (Guo et al., 2014, Mol Cell, 55(1): 15-30). Likewise,TRIM5δ, TRIM27, and TRIM32 rely on SUMO to remove Atxn1 82Q. An in vitroassay also confirms the SUMO E3 activity of TRIM27 towards Atxn1 82Q.Hence, TRIM proteins might employ similar mechanism to rid cells ofmisfolded proteins. The most relevant SUMO proteins for degradingmisfolded proteins are SUMO2/3. The poly-chains formed by SUMO2/3facilitate the recognition by the multiple SIMs on RNF4 (Tatham et al.,2008, Nat Cell Biol, 10: 538-546). Consistent with a role in proteinquality control, SUMO2/3 in unstressed cells are mainly un-conjugatedforms but become conjugated to target proteins after protein damagingstresses (Golebiowski et al., 2009, Sci Signal, 2: ra24; Saitoh andHinchey, 2000, J Biol Chem, 275: 6252-6258). Nevertheless, given thediversity among the TRIM proteins and the ubiquitin E3 ligase activityassociated with some (Meroni and Diez-Roux, 2005, Bioessays, 27:1147-1157), it is still possible that some TRIM proteins may primarilyfunction as ubiquitin E3s for misfolded proteins.

Currently, it is unclear why some TRIM proteins can degrade misfoldedproteins such as Atxn1 82Q, while others cannot. Also, among the TRIMproteins tested, TRIM11 possesses a remarkably potent activity to reduceAtxn1 82Q. It remains to be determined what may account for itsactivity. Some TRIM proteins can enhance the expression levels of Atxn182Q and especially Httex1p 97QP. This further underscores the functionaldiversity of these proteins. TRIM proteins can function as chaperones toprevent protein misfolding and as disaggregase to dissolve previouslyformed protein aggregates. These activities may in part account for theeffect of TRIM proteins to stabilize Atxn1 82Q and especially Httex1p97QP. This suggests another important usage of TRIM proteins in thetherapy of diseases associated with misfolded proteins. A number ofhuman diseases are linked closely to the degradation of mutant proteinsthat are partially functional. A notable example is cystic fibrosis(CF), which is caused by mutations in the gene cystic fibrosistransmembrane conductance regulator (CFTR). These mutations are degradedin the cytoplasm. Therapies are being developed to stabilize the mutantCFTR, allowing mutant CFTR to reach the member to fulfill its function.It is envisioned that using TRIM proteins may achieve such a goal in CFand other diseases associated with degradation of partially functionalproteins.

TABLE 2 Summary of the effect of cellular localization of TRIM proteinsand their co- localization with Atxn1 82Q. Other Isoforms Atxin1 82Qcommon used in Cellular aggregates Name names Domains Species this studylocalization Pattern colocalizaiton TRIM1 MID2, R B1 B2 CC h C diffuse,— FXY2, COS FN3 foci, RNF60 SPRY filament TRIM2 CMT2R, R B2 CC FIL h Cdiffuse, — RNF86 NHL foci TRIM3 BERP, R B2 CC FIL h C diffuse — HAC1,NHL RNF22, RNF97 TRIM4 RNF87 R B2 CC h C foci — SPRY TRIM5 RNF88 R B2 CCh γ C foci — SPRY (gamma does not have SPRY) TRIM6 RNF89 R B2 CC h C, Ndiffuse ** PRY SPRY TRIM7 GNIP, R B2 CC h C foci — RNF90 PRY SPRY TRIM8GERP, R B1 B2 CC h C, N foci *** RNF27 TRIM9 RNF91, R B1 B2 CC h C foci,— SPRING COS FN3 filament PRY SPRY TRIM10 RNF9, R B2 CC h C foci, —HERF1, PRY SPRY filament RFB30 TRIM11 BIA1, R B2 CC h C, N diffuse ***RNF92 PRY SPRY TRIM12 2310043C01Rik R B2 CC mouse C, N diffuse, — onlyfoci TRIM13 CAR, R B2 CC TM h Perinuclear diffuse, — LEU5, foci RFP2,DLEU5, RNF77 TRIM14 B2 CC h C, N foci — PRY/SPRY TRIM15 RNF93, R B2 CC hC foci — ZNFB7, PRY SPRY ZNF178 TRIM16 EBBP B2 CC h C, N, diffuse —PRY/SPRY perinuclear TRIM17 TERF, R B2 CC h C diffuse — RBCC, PRY SPRYRNF16 TRIM18 MID1, R B1 B2 CC h C filament — FXY, COS FN3 RNF59 PRY SPRYTRIM19 PML R B1 B2 CC h N foci *** TRIM20 PRYRIN, B2 CC h C diffuse,foci — MEFV PRY/SPRY TRIM21 Ro52, R B2 CC h C, N diffuse, *** SSA1, PRYSPRY foci, SSA/Ro, filament RNF81 TRIM22 STAF50, R B2 CC h short and Nfoci *** GPSTAF50, SPRY long RNF94 TRIM23 ARD1, R B1 B2 CC h C, N,diffuse, — ARFD1, ARF perinuclear foci RNF46 TRIM24 TIF1α, R B1 B2 CC hC, foci — TF1A, PHD BR perinuclear TIF1A, TIF1, PTC6, RNF82 TRIM25 EFP,Z147, R CC PRY h C diffuse, — RNF147, SPRY foci ZNF147 TRIM26 AFP, R B2CC h C diffuse, — RNF95, PRY SPRY foci ZNF173 TRIM27 RFP, R B2 CC h C, Nfoci *** RNF76 PRY SPRY TRIM28 KAP, R B1 B2 CC h N diffuse *** TIF1β,PHD BR TF1B, TIF1B, RNF96, PPP1R157 TRIM29 ATDC B1 B2 CC h C filament —TRIM30 RPT1, R B2 CC mouse C, N diffuse, *** RGD1563970 PRY/SPRY onlyfoci TRIM31 RNF, R B2 CC h C, N diffuse, # HCG1, foci HCGI, C6orf13TRIM32 HT2A, R B2 CC h C, N foci ** BBS11, NHL TATIP, LGMD2H TRIM33TIF1γ, R B1 B2 CC h N diffuse, *** TF1G, PHD BR foci TIF1G, ECTO, PTC7,RFG7 TRIM34 IFP1, R B2 CC h C foci — RNF21 SPRY TRIM35 HLS5, R B2 CC hC, N foci ** MAIR PRY SPRY TRIM36 RNF98, R B1 B2 CC h C filament —HAPRIN, COS FN3 RBCC728 SPRY TRIM37 MUL, R B2 CC h C foci — POB1, MATHTEF3 TRIM38 RoRet, R B2 PRY h C, N foci *** RNF15 SPRY TRIM39 TFP, R B2CC h C foci — RNF23 PRY SPRY TRIM40 RNF35 R B2 CC h C, N diffuse #TRIM41 RINCK R CC B2 CC h C foci — PRY SPRY (According to Nat immreview) TRIM42 T4A1, R B1 B2 CC h N/A N/A N/A PPP1R40 COS FN3 TRIM43 RB2 CC h N/A N/A N/A SPRY TRIM44 DIPB, B2 CC h C, N diffuse — MC7,HSA249128 TRIM45 RNF99 R B1 B2 CC h C foci — FIL NHL TRIM46 TRIFIC, R B2CC h C filament — GENEY COS FN3 SPRY TRIM47 GOA, R B2 CC h foci — RNF100PRY TRIM48 RNF101 R B2 SPRY h C. N diffuse # TRIM49 RNF18, R B2 SPRY hC, N diffuse — TRIM49A, TRIM49L2 TRIM50 R B2 CC h C foci — PRY SPRYTRIM51 SPRYD5A R B2 SPRY h C, N foci * TRIM52 RNF102 R B2 h C, N diffuse# TRIM53 R SPRY h N/A N/A N/A (According to Nat imm review) TRIM54 MURF,R B2 CC h C filament — RNF30, COS muRF3, MURF-3 TRIM55 MURF-2, RNF29, RB2 CC h C, N foci, *** muRF2 COS filament TRIM56 RNF109 R B2 CC h C, Ndiffuse, — foci TRIM58 BIA2 R B2 CC h C, N diffuse, — PRY SPRY fociTRIM59 TRIM57, R B2 CC TM h N/A N/A N/A MRF1, TSBF1, IFT80L, RNF104TRIM60 RNF33, R B2 CC h N/A N/A N/A RNF129 PRY SPRY TRIM61 RNF35 R B2 CCh N/A N/A N/A TRIM62 DEAR1 R B2 CC h C, N foci — PRY SPRY TRIM63 MURF1,R B2 CC h C filament — RF1, COS RNF28 TRIM64 C11orf28 R B2 CC h C, Ndiffuse *** SPRY TRIM65 4732463G12Rik R B2 CC h N diffuse *** SPRYTRIM66 TIF1δ,TIF1D, B1 B2 CC h N foci, — C11orf29, PHD BR diffuse TRIM67TNL R B1 B2 CC h N/A N/A N/A COS FN3 SPRY TRIM68 GC109, R B2 PRY h C, Ndiffuse — RNF137, SPRY SS-56, SS56 TRIM69 HSD-34, R CC PRY h C filament— HSD34, SPRY RNF36, Trif TRIM70 CC h N/A N/A N/A PRY/SPRY TRIM71LIN-41, R B1 B2 CC h N/A N/A N/A LIN41 FIL NHL TRIM72 MG53 R B2 CC h N/AN/A N/A PRY SPRY TRIM73 TRIM50B R B2 CC h C, N foci *** TRIM74 TRIM50C RB2 CC h C, N foci, ** diffuse TRIM75 R B2 CC h N/A N/A N/A PRY SPRYTRIM76 CMYA5, B CC FN3, h C diffuse — SPRYD2, PRY/SPRY C5orf10 — Noco-localization # Faintly distributed around aggregates * <5% cells **5-20% cells *** >20% cells

Soluble IS Total Detection WB fraction Subfamily WB WB flow WB TrimsTrim1 I — — — Normal S/IS Trim2 VII — — — Normal S Trim3 VII — ↓ —Normal S/IS Trim4 IV — ↓↓ Normal S/IS Trim5 IV — ↓↓ Normal S/IS Trim6 IV— ↓ None Trim7 IV — ↓ None Trim8 V — — — Normal S/IS Trim9 I ↓ ↓↓ ↓↓ LowS Trim10 IV — — ↓ IS Trim11 IV ↓↓↓ ↓↓↓ ↓↓↓ None Trim12 — — — Low ISTrim13 XI — ↓/— — Normal IS Trim14 F IV — ↓/— ↓ Normal IS Trim15 IV —↓/— ↓ Normal IS Trim16 F IV ↓ ↓ ↓ None Trim17 IV ↓ ↓↓ ↓ Normal S/ISTrim18 I — — — Normal S Trim19 V ↓ — ↓ Normal S/IS Trim20 F IV ↓↓ ↓↓↓↓↓↓ Low S Trim21 IV — ↓ ↓ Normal S/IS Trim22 IV — — ↓ Normal S/IS Trim23IX — — ↓ Low S/IS Trim24 VI — ↓ ↓↓ None Trim25 IV — — ↓ None Trim26 IV —↑ ↑ Normal IS Trim27 IV — — — Normal IS Trim28 VI — ↓ — Normal S Trim29— ↓ — Normal IS Trim30 — ↓↓ ↓↓ Low IS Trim31 V — — ↓ Normal S Trim32 VII— — — Normal IS Trim33 VI ↑ ↑ — None Trim34 IV — ↓ ↓ Normal IS Trim35 IV— — — Normal IS Trim36 I — ↑ None Trim37 VIII — ↑ None Trim38 IV — ↑ LowS/IS Trim39 IV — ↓ Normal S/IS Trim40 V — — Normal S Trim41 IV — —Normal S/IS Trim42 III ↑ ↑ ↑ Normal S/IS Trim43 IV — ↓↓ ↓ Normal ISTrim44 — ↓ — Normal S/IS Trim45 XI — ↓ — Normal IS Trim46 I — ↓ ↓ NormalS/IS Trim47 IV — ↑ ↓ Normal S/IS Trim48 IV — ↓ Low IS Trim49 IV ↓ ↓↓ ↓Low S/IS Trim50 IV — ↓↓ ↓ Normal S/IS Trim51 F IV — — — None Trim52 V ↓↓ Normal S Trim54 II — — — none Trim55 II — — ↑ Normal S Trim56 V — — —None Trim58 XI — — ↑ Normal S/IS Trim59 XI ↓ ↓ — Normal S/IS Trim60 IV —— ↑ None Trim61 V — — ↑ None Trim62 IV — — — None Trim63 II — — ↑ NormalTrim64 IV — ↑ — Normal S/IS Trim65 IV ↓ ↓↓ ↓ Normal S/IS Trim66 FIV — ↑↑ None Trim67 I — ↓ ↓/— Normal S/IS Trim68 IV — — ↓ Normal S Trim69 IV ↑↑ ↑ None Trim70 F IV — ↓↓ ↓↓ low S/IS Trim71 VII — — — None Trim72 IV —— ↑ Normal S/IS Trim73 V — — — Normal Trim74 V — ↓ ↓ Normal Trim75 IV —↓↓ ↓ Normal Trim76 — ↑ ↑ Normal S/IS Trim77 — — ↑ — No Change ↓ 10-25%↓↓ 25-50% ↓↓↓ >50% ↓/— Change < 10%

TABLE 4 Summary of the effect of TRIM proteins on Httex1p 97QP SubfamilySoluble WB IS WB Total flow Trim1 I — ↑ — Trim2 VII — — — Trim3 VII — ↓— Trim4 IV — ↑ — Trim5 IV — — — Trim6 IV — ↑ — Trim7 IV — ↑ — Trim8 V —↑ — Trim9 I — ↑ — Trim10 IV — ↑ — Trim11 IV ↓ ↓ ↓↓↓ Trim12 — ↑ ↑ Trim13XI — ↑ ↑ Trim14 F IV — ↑↑ ↑ Trim15 IV — ↑↑ — Trim16 F IV — ↑ ↓ Trim17 IV— ↑ — Trim18 I — ↑ — Trim19 V — ↑/— ↓ Trim20 F IV — ↑/— ↓ Trim21 IV — ↑↑ Trim22 IV — — — Trim23 IX — ↑ ↑ Trim24 VI — ↑ ↓ Trim25 IV — ↑ ↑ Trim26IV — ↑ ↑ Trim27 IV — ↑ ↑ Trim28 VI — ↑ ↑ Trim29 — — ↓ Trim30 — ↓ ↓↓Trim31 V — — — Trim32 VII — ↑ ↑ Trim33 VI — ↑ ↑ Trim34 IV — ↑ ↑ Trim35IV — ↑ ↑ Trim36 I — ↑ ↑ Trim37 VIII — ↑ ↑ Trim38 IV — ↑ ↑ Trim39 IV — ↑— Trim40 V — — ↑ Trim41 IV — ↑ ↑

Example 3: Delivery of Recombinant TRIM11 into Mammalian Cells Promotesthe Degradation of Misfolded Proteins

As described above, it has been demonstrated that members of thetripartite motif-containing (TRIM4) family play an important role in therecognition and degradation of misfolded proteins. Initially usingPML/TRIM19 as an example, it was shown that PML can specifically bind tomisfolded proteins via distinct regions that recognize structurefeatures commonly found in misfolded proteins. PML then uses its SUMO E3activity to tag the misfolded proteins with poly-SUMO2/3 chains. Thisallows misfolded proteins to be recognized by a SUMOylation-targetedubiquitin ligase (STUbL) RNF4, with the consequential ubiquitination andproteasomal degradation of misfolded proteins. It was further shown thatthis PML-RNF4-mediated sequential SUMOylation and ubiquitination systemplays an important role in the protection against neurodegenerativediseases.

Subsequently, the vast majority of all known human TRIM proteins weresurvey, and it was found that a substantially number of them are able tolocalize to the inclusion formed by misfolded proteins such aspathogenic ataxin 1 (Atxn1 82Q) and huntingtin (Htt 97Q) proteins. Bytesting representative TRIM proteins, it was shown that many TRIMproteins are also capable of degrading misfolded proteins in aSUMO-dependent manner. Of note, among the TRIM proteins that weretested, one TRIM proteins, TRIM11, exhibits a particularly strongactivity to reduce misfolded proteins.

In the experiments presented herein, it was sought to developrecombinant TRIM11 as an agent for degrading intracellular misfoldedproteins associated with neurodegeneration. For this, the HIVTat-derived peptide was used, which is able to deliver proteins intomammalian cells (FIG. 22 ). TRIM11 was fused with the Tat-derivedpeptide, the fusion protein was expressed in bacteria, and the proteinwas purified to homogeneity using affinity resin, followed by gelfiltration column. For comparison, Tat-peptide-fused SUMO2 protein wasalso purified in parallel.

HeLa cells were transfected with Atxn1 82Q-GFP, Atxn1 30Q, or Htt97Q-GFP, and were subsequently incubated with recombinant TRIM11 orSUMO2 proteins. As shown in FIG. 21A, treatment of HeLa cells withTRIM11 led to strong reduction in the levels of Atxn1 82Q. It also ledto strong reduction in the levels of Htt 97Q (FIG. 21B). In contrast,SUMO2 had minimal effect on the levels of Atxn1 82Q (FIG. 21C). Thesedata suggest that delivery of TRIM11 into mammalian cells reduces thelevels of misfolded proteins, providing a proof or concept evidence fortargeting the TRIM-RNF4 system for the therapy of neurodegeneration andother protein-misfolding diseases.

Example 4: Localization of RNF4 to Neuronal Inclusions in SCA1 and HDPatients

RNF4 deficiency in mice results in embryonic lethality (Hu et al, 2010,PNAS 107:15087-92), precluding the analysis of its deficiency on mousemodels of neurodegeneration. Previous studies showed that PML, alongwith SUMO and ubiquitin, co-localizes with neuronal inclusions inpolyglutamine disease patients (Dorval and Fraser; 2006, J BIol Chem281:9919-24; Martin et al., 2007, Nat Rev Neurosci 8:948-59; Skinner etal., 1997, Nature 389:971-4; Takahasi et al., 2003, Neurobiol Dis13:230-70), suggesting the involvement of PML in these diseases. Thedata presented herein analyzes the localization of RNF4 in post-mortembrain tissues of human SCA1 and HD patients.

The materials and methods employed in these experiments are nowdescribed.

HD patient tissues (globus pallidus) were provided by the Harvard BrainTissue Resource Center: AN06564, AN12127 and AN12029 (aggregatesobserved), and AN09048, AN19685, AN14942, AN13612 and AN17467 (noaggregates observed); SCA1 patient tissues (basis points) were obtained,National Ataxia Foundation. Immunohistochemistry and immunofluorecencewere performed as previously described with modifications (Duda et al.,2000, J Neuropathol Exp Neurol 59:830-41; Emmer et al., 2011, J BiolChem 286:35104-18). HD and SCA1 patient brains were embedded in paraffinand cut into 6 □m sections. Sections were stained for anti-RNF4 (#1:Rabbit, 11-25, 1:300, Sigma; #2: Goat, C15, 1:25, Santa Cruz),anti-Huntingtin (mouse, MAB5374, 1:500; Millipore), anti-ubiquitin(mouse, Ubi-1, MAB1510, 1:2,000; Millipore), and anti-polyQ (mouseMAB1574, 1C2, 1:1,000; Millipore) as indicated. Control rabbitantibodies were used to confirm the specificity of anti-RNF4 staining.

The results of the experiments are now described.

When detected in patient neurons without inclusions, RNF4 tended todistribute diffusely throughout the nucleus or form nuclear foci (FIG.23 ). In the two cases of SCA1 that were examined, nuclear inclusionsreactive to an anti-polyQ antibody (1C2) were present. RNF4 was found infive out of sixteen and four out of seventeen 1C2-reactive nuclearinclusions, respectively (FIG. 24 ).

Among the HD patients, cytoplasmic inclusions reactive to eitheranti-huntingtin or anti-ubiquitin antibody were present in the globuspallidus region in three out of eight patient samples examined. This wasin agreement with previous observations that nuclear inclusions wererare in adult-onset HD cases (DiFiglia et al., 1997, Science277:1990-3). Nevertheless, RNF4 co-localized with approximately 20% ofthe inclusions in the globus pallidus region based on the results withtwo separate anti-RNF4 antibodies (FIG. 25 and FIG. 26 ). The inclusionscontaining RNF4 tended to show RNF4 immunoreactivity surrounded by aring of huntingtin or ubiquitin signals (FIG. 25 and FIG. 26 ). Thepartial co-localization of RNF4 with the polyQ aggregates in SCA1 and HDpatients is reminiscent of the partial co-localization of PML with polyQaggregates (Skinner et al., 1997, Nature 389:971-4; Takahashi et al.,2003, Neurobiol Dis 13:230-7), and it may reflect the blockage of thePML/TRIM-RNF4 system in the disease-affected neurons.

Example 5: Molecular Chaperone and Protein Diaggregase Activities ofTRIM Proteins

The data described herein demonstrates that TRIM11 can function as amolecular chaperone and disaggregase. In one aspect, TRIM11 can preventaggregate formation. On the other hand, TRIM11 is not only able torefold stress-induced non-amyloid aggregates (luciferase and GFPaggregates), but also disaggregate amyloid aggregates (Atxn1 82Qaggregates and alpha-Synuclein fibrils). Further, it is also shownherein that TRIM11 is also a SUMO E3 ligase that can SUMOylate Atxin182Q and subsequent degradation. Therefore, TRIM11 may serve as a linkbetween protein disaggregation and degradation.

The materials and methods employed in these experiments are nowdescribed.

siRNA Transfection

Mouse TRIM11 siRNA (sc-76735) was purchased from Santa Cruz. In thefirst day, hippocampal neuron cells (15000 cells/well) were plated in 96well plates with plating medium. In the second day (about 18 hours afterplating), completely change the plating medium to neuronal medium. Inthe third day, siRNA (1 pmol) was transfected into cells byLipofectamine RNAiMAX. The transfection methods were carried outaccording to the manufacturer's instructions.

Cell Culture

HCT16 cells were cultured with Mccoy 5A medium. A549 cells were culturedwith RPMI1640 medium. HeLa and HEK293T cells were cultured with DMEMmedium.

These culture mediums all contain 10% Fetal Bovine Serum (FBS). Primaryneuron cells were obtained. Neuron cells were cultured according topreviously described methods. Simply, the cells were first plated withplating medium (Combine Neurobasal medium, B27, GlutaMAX,penicillin/streptomycin and 10% FBS by the indicated dilution ratios).After 18-24 h, completely change the plating medium to neuronal medium(Combine Neurobasal medium, B27, GlutaMAX and penicillin/streptomycin bythe indicated dilution ratios). Except notification, all cells weremaintained at 37° C. in a humidified 5% CO₂ atmosphere.

Immunofluorescence

Cells plated on coverslips were fixed with 4% paraformaldehyde for 10minutes at room temperature. Cells were further permeabilized withmethanol for 10 minutes at 20° C. Cells were washed with PBS and thenblocked by 2% bovine serum albumin (BSA) for 30 min at room temperature.Cells were incubated with the primary antibody overnight at 4° C.,followed by incubation with a fluorescent secondary antibody for 1 hourat room temperature. Finally, the coverslips were mounted to glassslides with mounting medium containing 4′,6-diamidino-2-phenylindole(DAPI) (Vector Laboratories; H-1200). For antibodies dilution, anti-HA(1:100), anti-p-a-Syn (1:100) and anti-p62 (1:200) were applied.

Antibodies

Anti-TRIM11 (ABC926) antibody was purchased from Millipore. Monoclonalanti-Flag antibody, rabbit Flag antibody and anti-Flag agarose beadswere purchased from Sigma. Anti-HA affinity matrix (clone 3F10,11815016001) was purchased from Roche. Anti-HSF1 (sc-9144) was purchasedfrom Santa Cruz. Anti-a-Synuclein Phopho-Ser129 (825701) was purchasedfrom Biolegend. Anti-Hsp70 (ADI-SPA-810-D) was purchased from Enzo.Anti-a-Synuclein (2642) and anti-Hsp90 (4874) was purchased from Cellsignaling technology.

Protein Fractionation, Filter Retardation Assay and Immunoblotting

Cells were lysed with the lysis buffer (50 mM Tris, pH 8.8, 100 mM NaCl,5 mM MgCl₂, 0.5% IGEPAL CA-630, 1 mM DTT, 250 IU/ml benzonase (Sigma), 1mM PMSF and 1× complete protease cocktail (Roche)) for 30 minutes onice. The supernatant was obtained by centrifuging 13000 rpm for 15-20minutes at 4° C. The pellet was further resuspended in the pellet buffer(20 mM Tris, pH 8.0, 15 mM MgCl₂, 1 mM DTT, 250 IU/ml benzonase, 1 mMPMSF and 1×complete protease cocktail) for 30 minutes on ice, followedby directly boiling with 2% SDS buffer. Protein concentration wasmeasured by Bradford assay (Bio-Rad Labs). All protein samples weresubjected to immunoblotting by SDS-PAGE. The supernatant was consideredas a soluble fraction. The pellet was considered as an insolublefraction (SDS-soluble). The other portion was subjected to filterretardation assay. Simply, the pellet samples were filtered through amembrane with 0.2 μM pore size, so that the SDS-resistant aggregatesretained on the membrane were analyzed by immunoblotting.

Protein Purification

Flag-Atxn1-82Q-HA was transfected in 293T cells and purified byanti-Flag M2 beads. For getting highly purified proteins, the beads wereextensively washed with increased concentrations of NaCl.

His-Luciferase was expressed in BL21 DE3 cells purified. To generateimmobilized native or denatured luciferase, native luciferase was firstpurified from bacterial cell lysates according to the manufacturer'sinstructions. Second, denatured luciferase was generated by incubatingnative luciferase with 8 M urea for 5 minutes

In Vivo and In Vitro Sumoylation Assays

For in vivo sumoylation assays, cells were transfected with theindicated plasmids. After 48 hours, cells were lysed in lysis buffer (50mM Tris-Cl, pH 7.4, 150 mM NaCl, 0.5% Trition, 1 mM DTT, 1 mM PMSF and1× complete protease cocktail) supplemented with 2% SDS and 50 mM DTT.Cell lysates were further boiled at 95° C. for 10 minutes. One aliquotwas saved for input. The rest of cell lysates were diluted 10-fold inlysis buffer and then incubated with anti-HA beads at 4° C. overnight.The beads were extensively washed and analyzed by immunoblotting withthe indicated antibodies. For in vitro sumoylation assays, His-SUMO-2(UL-753), UbcH9 (E2-465) and SUMO E1 (E-315) were purchased from BostonBiochem.

Plasmids

Flag-TRIM11 was constructed by inserting KpnI/XbaI TRIM11 cDNA intoKpnI/XbaI digested pcDNA3.1-Flag vector. Flag-TRIM11 mutation (12/13EEto 12/13AA) was generated by site-directed mutation. GST-TRIM11 wasconstructed by inserting BglII/SalI TRIM11 cDNA into BamHI/SalI digestedpGEX-1λT vector. GFP-Hsp70 and GFP-TRIM 11 were constructed by insertingHsp70 and TRIM11 cDNA into pEGFP-C1 vector. All the constructs wereverified by DNA sequencing.

Luciferase Reactivation Assay

To generate aggregates, firefly luciferase (100 nM) in luciferaserefolding buffer (LRB; 25 mM HEPES-KOH [pH 7.4], 150 mM KAOc, 10 mMMgAOc, 10 mM DTT) was heated at 45° C. for 8-10 minutes. Aggregatedluciferase (10 nM) was incubated with the indicated concentrations ofTRIM11 or other proteins at 25° C. for 90 minutes. ForHsp104/Hsp70-Hsp40 di-chaperone system, 5 mM ATP and an ATP regenerationsystem (1 mM creatine phosphate, 0.5 uM creatine kinase) were required.For in vivo luciferase refolding assay, cells in 96 well plate weretransiently transfected with wild type luciferase. After 24 hours, cellswere heated at 42° C. or 45° C. for 1 hour or 30 minutes, respectively.Prior to heat shock, 20 μg/ml cycloheximide was added into culturemedium. After heat shock, cells were transferred to 37° C. incubator foranother 1.5 or 3 hours. Luciferase activity was measured with PromegaLuciferase System.

GFP Disaggregation Assay

To generate aggregates, GFP (4.5 μM) in buffer A (20 mM Tris-HCl, pH7.5, 100 mM KCl, 20 mM MgCl₂, 5 mM DTT, 0.1 mM EDTA, 10% (v/v) glycerol)was incubated for 15 minutes at 85° C. GFP aggregates (0.45 μM) wereincubated with the indicated proteins with different amounts at 25° C.for 60 minutes. Disaggregation of GFP aggregates was detected bymeasuring fluorescence at 510 nm upon excitation at 395 nm (InfiniteM200 pro).

Reagents

Luciferase (L9506), Mg-ATP (A9187), phosphocreatine (P1937) and creatinekinase (C3755) were purchased from Sigma. KRIBB11 (385570) was purchasedfrom Millipore. Beta-Amyloid (1-42) (RP10017) was purchased fromGenScript.

The results of the experiments are now described.

PML (TRIM19) SUMOylated misfolded protein that can be recognized by RNF4to be degraded through proteasome. However, it is unknown whether TRIM11is also a SUMO E3 ligase. According to the structural analysis of TRIMs,two highly conserved glutamates (Glu9 and Glu10) of TRIM25 are requiredfor its ubiquitin E3 ligase activity. Therefore mutated TRIM11(Glu12/Glu13 to Ala12/Ala13) were generated that lacked E3 ligaseactivity (FIG. 27A and FIG. 27B). In vivo SUMOylation assay showed thatAtxn1 82Q was efficiently SUMOylated by wild type TRIM11, as well as PML(FIG. 27A). To further confirm this, in vitro SUMOylation assay showedthat purified Atxn1 82Q could be significantly SUMOylated by TRIM11.Therefore, TRIM11 was also a SUMO E3 ligase for Atxn1 82Q. In cells,TRIM11 like Hsp70 was mainly localized in the cytoplasm (FIG. 28A andFIG. 28B). Intriguingly, TRIM11 or Hsp70 could be recruited into theaggregates of Atxn1 82Q (FIG. 28C and FIG. 28D), suggesting that theremight be an interaction between TRIM11 and Atxn1 82Q. To test this, pulldown analysis presented that TRIM11 selectively bound to Atxn1 82Q (FIG.29A). Importantly, TRIM11 preferentially interacted with pathologic formAtxn1 82Q, not Atxn1 30Q (FIG. 29B). Therefore it was hypothesized thatTRIM11 had a potential to selectively bind to misfolded proteins. Toinvestigate the prediction, native or denatured luciferase beads werefurther generated and then a pull down assay was performed. As shown inFIG. 29C, in contrast to control GST proteins, TIRM11 specifically boundto denatured luciferase, which indicated that TRIM11 was capable ofbinding misfolded proteins.

It has been demonstrated that Hsp70, a molecular chaperone, can suppressthe expression of pathology associated Atxn1 82Q in SCA1 mice.Additionally, Hsp70 reduced the protein level of the detergent-insolublefraction of Atxn1 82Q, which was consistent with the results presentedherein (FIG. 28E). It was next investigated whether there was asimilarity between TRIM11 and Hsp70 for aggregate formation. To studythis, the solubilized feature of Atxn1 82Q was analyzed by detergentfractionation. As show in FIG. 28E, TRIM11, like Hsp70, reduced thedetergent-insoluble fraction of Atxn1 82Q, suggesting that TRIM11 couldcontrol protein aggregation. Moreover, MG132 treatment moderatelyincreased the insoluble Atxn1 82Q fraction (FIG. 28E), which wasconsistent with the previous report that the proteasome is necessary forcontrolling Atxn1 82Q aggregate formation. Interestingly, when Atxn1 82Qwas co-expressed with wild type TRIM11 or mutant TRIM11, the mutantTRIM11 had a lower ability to reduce the detergent-insoluble fraction ofAtxn1 82Q by comparing with wild type TRIM11 (FIG. 28F), suggesting thatE3 ligase activity of TRIM11 was required for the reduction of Atxn1 82Qaggregates. To further test whether TRIM11 had an effect on amyloid likeaggregates in cells, wild type or mutant TRIM11 was transfected into thecells and ThT staining showed that wild type and mutant TRIM11 couldboth down-regulate the level of amyloid like aggregates (FIG. 28G).Stable overexpression of Atxn1 82Q moderately enhanced the ThT staining(FIG. 30A). Similarly, TRIM11 could also reduce the detergent-insolublefractions of Atxn1 82Q in stable cells (FIG. 30B). Importantly, wildtype TRIM11 had a stronger ability than mutant TRIM11 could to reducethe cellular aggregates (FIGS. 30C and 30D).

Due to the similarity of Hsp70 and TRIM11, it was hypothesized thatTRIM11 might function as molecular chaperone for controlling proteinaggregation. Generally, chaperones have a capacity of preventingaggregation-prone misfolded proteins. This is the most primary andeffective way to control protein aggregation. Therefore, the preventionfunction of TRIM11 in the formation of aggregate was investigated.Luciferase activity was rapidly decreased without chaperone in responseto heat shock (FIG. 31A). However, incubation of TRIM11 as well as Hsp70could efficiently protect luciferase from heat inactivation (FIG. 31A).Similarly, TRIM11 also protect GFP proteins against heat (FIG. 31C).These results suggested that TRIM11 might function as molecularchaperone like Hsp70. In cells, stable overexpression of TRIM11 was ableto moderately protect luciferase against heat shock (FIG. 31C and FIG.31D). What's more, TRIM11 could also obviously recover the heatinactivation of luciferase (FIG. 31C and FIG. 31D), which furtherconfirmed the chaperone like function of TRIM11. Importantly, TRIM11overexpression did not change the protein level of Hsp70 (FIG. 31E).Next, Alzheimer disease associated beta-amyloid (1-42) was used as asubstrate to study the prevention function of TRIM11. As shown in FIG.31F, TRIM11 could inhibit amyloid fiber formation by ThT analysis.Additionally, Atxn1 82Q was purified to test the process of aggregateformation. Control protein GST could not prevent Atxn1 aggregateformation, while TRIM11 efficiently blocked the formation of aggregate(FIG. 31G). Moreover, TRIM11 could also prevent amyloid like aggregateof Atxn1 82Q (FIG. 31G). It is known that p53 is prone to form aggregatein vitro. As shown in FIG. 31H, TRIM11 significantly prevented p53 fromdenaturation. Intriguingly, p53 could be SUMOylated by TRIM11 in vitro(FIG. 27C) and SUMOylation of p53 could block amyloid like aggregate butpromoted oligomer formation. To sum up, TRIM11 may function as amolecular chaperone to prevent aggregate formation.

To determine if TRIM11 could be upregulated in response to heat shockHCT116 cells stably expressing vector or TRIM11 were used. In controlstable cells, TRIM11 was increased during the recovery after heat shock(FIG. 32A). However, in TRIM11 expressing cells, exogenous TRIM11protein could not be upregulated (FIG. 32B), meaning that the upregulation of TRIM11 induced by heat was not due to the change ofprotein stability. Heat-induced TRIM11 up regulation was furtherconfirmed in HeLa cells (FIG. 32C). Because many stress can induceprotein misfolding, whether TRIM11 could be induced by other stress wasexamined. As shown in FIGS. 30D and 30E, the protein level of TRIM11 wasupregulated in response to As₂O₃ and H₂O₂ treatment. The mRNA level ofTRIM11 could be induced in response to heat shock (FIG. 32F), which issimilar with Hsp70. To investigate the mechanisms by which TRIM11 wasinduced by heat shock, A549 cells were generated which stably expressHSF1, a key transcriptional factor to control heat responsive proteins.Surprisingly, overexpression of HSF1 down-regulated TRIM11 protein levelwith or without heat shock treatment (FIG. 32G), suggesting that HSF1was possible not required for regulating the transcription of TRIM11.

Another key transcriptional factor, p53, can be activated during theheat shock response. p53 is also able to directly increase thetranscription of TRIMs, for example TRIM21 and TRIM24. Therefore, it wasinvestigated whether TRIM11 could be controlled by p53 in response toheat shock. As shown in FIG. 33A, TRIM11 was increased in response toheat shock in p53 wild type but not p53 null HCT116 cells. Accordingly,the mRNA level of TRIM11 only was enhanced in p53 wild type HCT116 cells(FIG. 33B), suggesting that p53 contributed to TRIM11 transcription. Tofurther confirm the importance of p53, the protein and mRNA level ofTRIM11 could not be upregulated in A549 cells stably expressing p53shRNA (FIG. 33C). Similar phenomenon was confirmed again in p53knockdown HCT116 cells (FIG. 33D). Together, these results stronglyimplied that p53 might be a key factor to upregulate TRIM11 in heatshock response. HSF1 is considered as a safeguard for cell survivalfollowing heating stress. KRIBB11, a chemical inhibitor, can be used toinhibit HSF1 activity. As shown in FIG. 33E and FIG. 33F, with KRIBB11treatment, p53 nulls were more sensitive to heat shock, which impliedthat p53 also contributed to cell survival in response to heatingstress.

Hsp70 may promote the dissolution of some kinds of protein aggregates.Next, it was investigated whether TRIM 11 could disaggregate proteinaggregates. As expected, TRIM11 resolubilized heat-inactivatedluciferase from insoluble aggregates (FIG. 34A) and recovered luciferaseactivity in a dose-dependent manner (FIG. 34B). Also, the solubilizedfunction of TRIM11 was further confirmed using preformed GFP aggregatesas substrates (FIG. 34C and FIG. 34D). These results suggested that TRIM11 could disaggregate disordered aggregates. Next, assays were performedusing Atxn1 82Q aggregates as substrates. As shown in FIG. 34E, TRIM11could efficiently resolubilized Atxn1 82Q aggregates. Notably,Hsp70/Hsp40 di-chaperone only disaggregated amyloid like structure ofAtxn1 82Q into the pellet (FIG. 34F), suggesting that TRIM11 might actin a different way. As expected, TRIM11, as well as Hsp104,significantly recovered amyloid like structure into the supernatant(FIG. 34G).

To determine which functional domain of TRIM11 was required fordisaggregation activity of TRIM11 heated luciferase aggregates were usedas substrates. As shown in FIG. 35B, TRIM11 could efficiently recoverheat inactivation of luciferase activity, but RBC or B30.2 fragments ofTRIM11 had weaker reactivation ability. Consistently, in sedimentationassay, TRIM11 had a stronger activity than its two fragments toresolubilize preformed luciferase aggregates (FIG. 35C). Further, eachsingle domain almost lost the refolding activity by comparing with fulllength TRIM11 (FIG. 35D). Furthermore, full length TRIM11 very stronglyinteracted with Atxn1 82Q, but RBC or B30.2 did not bound to Atxn1 82Q(FIG. 36A). Similarly, single domain of TRIM 11 did not bind to Atxn182Q (FIG. 36B). These results strongly suggested that binding tosubstrates might be required for TRIM11 disaggregation function.

It was next investigated whether SUMO E3 ligase activity is required forprotein disaggregation. Here mutant TRIM11 was used to test itsdisaggregation activity. As shown in FIG. 37A, mutant TRIM11 maintainedthe ability to prevent luciferase from heat inactivation like wild typeTRIM11. Moreover, mutant TRIM11 also had a similar potential with wildtype TRIM11 to recover denatured luciferase activity (FIG. 37B). MutantTRIM11 was still able to selectively bind to denature luciferase (FIG.37C). All these results indicated that in vitro, TRIM11 performed itsdisaggregation function independently of its E3 activity. Notably,mutant TRIM11 was largely localized in the nucleus (FIG. 37D), which wasdifferent from wild type TRIM11. Further, mutant TRIM11 could also beco-localized with Atxn1 82Q.

Previous studies showed that Hsp110, Hsp70, and Hsp40, the metazoanprotein disaggregase system, could not efficiently disaggregate amyloid.Therefore, it was investigated whether TRIM11 could disaggregate amyloidfiber. Here alpha-synuclein was applied as a client. Firstly, it wasdetermined whether TRIM11 could also prevent alpha-Synuclein fiberformation. As shown in FIG. 38A, TRIM11, as well as Hsp70 and Hsp104,efficiently inhibit the formation of alpha-Synuclein amyloid fiber (FIG.38A). Also, the inhibition was a dose-dependent manner (FIG. 38B).Indeed, electron microscopy (EM) revealed that alpha-Synuclein fiberswere exhibited by control GST protein, whereas no fiber observed byTRIM11 (FIG. 38C). Next, alpha-Synuclein fibers were used to study thedisaggregation of TRIM11. As shown in FIG. 38D, with TRIM11 or mutantHsp104 treatment, solubilization of alpha-Synuclein fibers increased ina dose-dependent manner. Accordingly, fiber disassembly was obvious withTRIM11 or Hsp104 treatment by ThT fluorescence (FIG. 38E).

There are over 70 TRIM family members with common N-terminus anddifferent C-terminus. Therefore, next whether other TRIM proteins alsohad similar function like TRIM11 was investigated. Therefore, TRIM21 wasselected because it shares the same domains with TRIM11. In vitro pulldown assay revealed that TRIM21 also preferentially bound to denaturedluciferase (FIG. 39A). Similarly, TRIM21 could moderately solubilizedheated luciferase aggregates (FIG. 39B) and recovered heat inactivationof luciferase (FIG. 39C). TRIM21 also was able to protect luciferaseagainst heat inactivation (FIG. 39D). PML could degrade Atxn1 82Qaggregates through proteasome. So to investigate whether disaggregationand degradation of Atxn1 aggregates were coupled by PML, PML from waspurified 293T cells (FIG. 40A). As shown in FIG. 40B, PML could recoverheat inactivation of GFP fluorescence in a dose-dependent manner.However, the recover ability was weaker than TRIM 11 (FIG. 40C). Severalfragments of PML were also purified from 293T cells (FIG. 40D).Interestingly, one fragment (361-633) of PML might be necessary for thereactivation of heated GFP aggregates (FIG. 40E).

To better understand the role of TRIM11 in controlling formation ofalpha-Synuclein aggregates, mouse primary hippocampal neurons were usedas a model. Alpha-Synuclein fibrils (PEF) were generated with GST orTRIM11 in vitro (GST-PEF and TRIM11-PEF). Two weeks after PEF addition,about 30% neuron death induced by PEF aggregates (FIG. 41A). However,TRIM11-PEF has a lower toxic to neurons (FIG. 41A). Indeed,immunofluorescence revealed that there were significant alpha-Synucleinaggregates that recapitulated features of the Lewy bodies in Parkinson'sdisease brains, whereas there were no big aggregates following additionof TRIM11-PEF (FIG. 41 ), which further showed that TRIM11 had aprevention function in formation of alpha-Synuclein fibers. Notably, intwo kinds of neurons (cortical and hippocampal neurons), TRIM11 could beup-regulated in response to heat shock (FIG. 42A and FIG. 42B).Moreover, the mRNA level of TRIM11 was also increased in hippocampalneurons (FIG. 42C). It was of interest that TRIM11 was likely involvedin controlling neurodegenerative disease.

The disclosures of each and every patent, patent application, andpublication cited herein are hereby incorporated herein by reference intheir entirety. While this invention has been disclosed with referenceto specific embodiments, it is apparent that other embodiments andvariations of this invention may be devised by others skilled in the artwithout departing from the true spirit and scope of the invention. Theappended claims are intended to be construed to include all suchembodiments and equivalent variations.

What is claimed is:
 1. A composition for treating or preventing adisease or disorder associated with misfolded protein or proteinaggregates, the composition comprising a modulator of one or more TRIMproteins.
 2. The composition of claim 1, wherein the modulator increasesthe expression or activity of the one or more TRIM proteins.
 3. Thecomposition of claim 1, wherein the modulator is at least one of thegroup consisting of a chemical compound, a protein, a peptide, apeptidomemetic, an antibody, a ribozyme, a small molecule chemicalcompound, a nucleic acid, a vector, and an antisense nucleic acid. 4.The composition of claim 1, wherein the modulator increases theexpression or activity of at least one selected from the groupconsisting of human TRIM3, TRIM4, TRIM5, TRIM6, TRIM7, TRIM9, TRIM 11,TRIM13, TRIM14, TRIM15, TRIM16, TRIM17, TRIM19 (also referred to hereinas “PML”), TRIM20, TRIM21, TRIM24, TRIM25, TRIM27, TRIM28, TRIM29,TRIM32, TRIM34, TRIM39, TRIM43, TRIM44, TRIM45, TRIM46, TRIM49, TRIM50,TRIM52, TRIM58, TRIM59, TRIM65, TRIM67, TRIM69, TRIM70, TRIM74 andTRIM75; and mouse TRIM30.
 5. The composition of claim 1, wherein thecomposition comprises an isolated peptide comprising one or more TRIMproteins.
 6. The compositing of claim 5, wherein the isolated peptidefurther comprises a cell penetrating peptide (CPP) to allow for entry ofthe isolated peptide into a cell.
 7. The composition of claim 6, whereinthe CPP comprises the protein transduction domain of HIV tat.
 8. Thecomposition of claim 1, wherein the composition comprises an isolatednucleic acid molecule encoding one or more TRIM proteins.
 9. Thecomposition of claim 1, wherein the disease or disorder is a polyQdisorder.
 10. The composition of claim 1, wherein the disease ordisorder is a neurodegenerative disease or disorder selected from thegroup consisting of Spinocerebellar ataxia (SCA) Type 1 (SCA1), SCA2,SCA3, SCA6, SCA7, SCA17, Huntington's disease,Dentatorubral-pallidoluysian atrophy (DRPLA), Alzheimer's disease,Parkinson's disease, amyotrophic lateral sclerosis (ALS), atransmissible spongiform encephalopathy (prion disease), a tauopathy,and Frontotemporal lobar degeneration (FTLD).
 11. The composition ofclaim 1, wherein the disease or disorder is selected from the groupconsisting of AL amyloidosis, AA amyloidosis, Familial Mediterraneanfever, senile systemic amyloidosis, familial amyloidotic polyneuropathy,hemodialysis-related amyloidosis, ApoAI amyloidosis, ApoAII amyloidosis,ApoAIV amyloidosis, Finnish hereditary amyloidosis, lysozymeamyloidosis, fibrinogen amyloidosis, Icelandic hereditary cerebralamyloid angiopathy, type II diabetes, medullary carcinoma of thethyroid, atrial amyloidosis, hereditary cerebral hemorrhage withamyloidosis, pituitary prolactinoma, injection-localized amyloidosis,aortic medial amyloidosis, hereditary lattice corneal dystrophy, cornealamyloidosis associated with trichiasis, cataract, calcifying epithelialodontogenic tumor, pulmonary alveolar proteinosis, inclusion-bodymyostis, and cuteaneous lichen amyloidosis.
 12. The composition of claim1, wherein the disease or disorder is cancer associated with p53 mutantaggregates.
 13. A method for treating or preventing a disease ordisorder associated with misfolded protein or protein aggregates in asubject in need thereof, the method comprising administering to thesubject a composition comprising a modulator of one or more TRIMproteins.
 14. The method of claim 13, wherein the modulator increasesthe expression or activity of the one or more TRIM proteins
 15. Themethod of claim 13, wherein the modulator is at least one selected fromthe group consisting of a chemical compound, a protein, a peptide, apeptidomemetic, an antibody, a ribozyme, a small molecule chemicalcompound, a nucleic acid, a vector, and an antisense nucleic acid. 16.The method of claim 13, wherein the modulator increases the expressionor activity of at least one selected from the group consisting of humanTRIM3, TRIM4, TRIM5, TRIM6, TRIM7, TRIM9, TRIM 11, TRIM13, TRIM14,TRIM15, TRIM16, TRIM17, TRIM19 (also referred to herein as “PML”),TRIM20, TRIM21, TRIM24, TRIM25, TRIM27, TRIM28, TRIM29, TRIM32, TRIM34,TRIM39, TRIM43, TRIM44, TRIM45, TRIM46, TRIM49, TRIM50, TRIM52, TRIM58,TRIM59, TRIM65, TRIM67, TRIM69, TRIM70, TRIM74 and TRIM75; and mouseTRIM30.
 17. The method of claim 13, wherein the composition comprises anisolated peptide comprising one or more TRIM proteins.
 18. The method ofclaim 17, wherein the isolated peptide further comprises a cellpenetrating peptide (CPP) to allow for entry of the isolated peptideinto a cell.
 19. The method of claim 18, wherein the CPP comprises theprotein transduction domain of HIV tat.
 20. The method of claim 13,wherein the composition comprises an isolated nucleic acid moleculeencoding one or more TRIM proteins.
 21. The method of claim 13, whereinthe disorder is a polyQ disorder.
 22. The method of claim 13, whereinthe disease or disorder is a neurodegenerative disorder elected from thegroup consisting of Spinocerebellar ataxia (SCA) Type 1 (SCA1), SCA2,SCA3, SCA6, SCA7, SCA17, Huntington's disease,Dentatorubral-pallidoluysian atrophy (DRPLA), Alzheimer's disease,Parkinson's disease, amyotrophic lateral sclerosis (ALS), atransmissible spongiform encephalopathy (prion disease), a tauopathy,and Frontotemporal lobar degeneration (FTLD).
 23. The method of claim13, wherein the disease or disorder is selected from the groupconsisting of AL amyloidosis, AA amyloidosis, Familial Mediterraneanfever, senile systemic amyloidosis, familial amyloidotic polyneuropathy,hemodialysis-related amyloidosis, ApoAI amyloidosis, ApoAII amyloidosis,ApoAIV amyloidosis, Finnish hereditary amyloidosis, lysozymeamyloidosis, fibrinogen amyloidosis, Icelandic hereditary cerebralamyloid angiopathy, type II diabetes, medullary carcinoma of thethyroid, atrial amyloidosis, hereditary cerebral hemorrhage withamyloidosis, pituitary prolactinoma, injection-localized amyloidosis,aortic medial amyloidosis, hereditary lattice corneal dystrophy, cornealamyloidosis associated with trichiasis, cataract, calcifying epithelialodontogenic tumor, pulmonary alveolar proteinosis, inclusion-bodymyostis, and cuteaneous lichen amyloidosis.
 24. The method of claim 13,wherein the disease or disorder is cancer associated with p53 mutantaggregates.
 25. The method of claim 13, wherein the method comprisesadministering the composition to at least one neural cell of thesubject.
 26. A composition for treating or preventing a disease ordisorder associated with degradation of functional mutant protein, thecomposition comprising a modulator of one or more TRIM proteins.
 27. Thecomposition of claim 26, wherein the modulator increases the expressionor activity of the one or more TRIM proteins.
 28. The composition ofclaim 26, wherein the modulator is at least one of the group consistingof a chemical compound, a protein, a peptide, a peptidomemetic, anantibody, a ribozyme, a small molecule chemical compound, a nucleicacid, a vector, and an antisense nucleic acid.
 29. The composition ofclaim 26, wherein the disease or disorder is cystic fibrosis.
 30. Amethod for treating or preventing a disease or disorder associated withdegradation of functional mutant protein in a subject in need thereof,the method comprising administering to the subject a compositioncomprising a modulator of one or more TRIM proteins.
 31. The method ofclaim 30, wherein the modulator increases the expression or activity ofthe one or more TRIM proteins
 32. The method of claim 30, wherein themodulator is at least one selected from the group consisting of achemical compound, a protein, a peptide, a peptidomemetic, an antibody,a ribozyme, a small molecule chemical compound, a nucleic acid, avector, and an antisense nucleic acid.
 33. The method of claim 30,wherein the disease or disorder is cystic fibrosis.
 34. A compositionfor treating or preventing a disease or disorder associated withmisfolded protein or protein aggregates, the composition comprising amodulator of one or more SUMO-targeted ubiquitin ligase (STUbl).
 35. Thecomposition of claim 34, wherein the modulator increases the expressionor activity of one or more STUbLs.
 36. The composition of claim 34,wherein the modulator is at least one of the group consisting of achemical compound, a protein, a peptide, a peptidomemetic, an antibody,a ribozyme, a small molecule chemical compound, a nucleic acid, avector, and an antisense nucleic acid.
 37. The composition of claim 34,wherein the modulator increases the expression or activity of RNF4. 38.A method for treating or preventing a disease or disorder associatedwith misfolded protein or protein aggregates in a subject in needthereof, the method comprising administering to the subject acomposition comprising a modulator of one or more STUbLs.
 39. The methodof claim 38, wherein the modulator increases the expression or activityof one or more STUbLs.
 40. The method of claim 38, wherein the modulatoris at least one of the group consisting of a chemical compound, aprotein, a peptide, a peptidomemetic, an antibody, a ribozyme, a smallmolecule chemical compound, a nucleic acid, a vector, and an antisensenucleic acid.
 41. The method of claim 38, wherein the modulatorincreases the expression or activity of RNF4.
 42. A method for producinga recombinant protein comprising administering a modulator of one ormore TRIM proteins to cell modified to express a recombinant protein.43. The method of claim 42, wherein the modulator comprises an isolatedpeptide comprising one or more TRIM proteins.
 44. The method of claim42, wherein the modulator comprises an isolated nucleic acid moleculeencoding one or more TRIM proteins.